Thunderwing!
by Darkryt Orbinautz
Summary: When Twilight finds a new symbiosis partner in Trixie, it leads to a confrontation with Shining Armor she didn't want, and the two mares let their resentment get the better of them and unleash Thunderwing, an ancient horror. Who is gonna fix it? Um, t-there ya go, really. Who. WHO. Who is gonna fix it, who will make right! As he travels cross the galaxy at twice the speed of light!
1. Breakaway

**Transformers and My Little Pony are the properties of Hasbro.**

**Doctor Who and related concepts are the properties of The BBC broadcasting network.**

**This is a non-profit work made by an independent contractor outside of ****any**** company's official notice intended for non-profit entertainment and speculative purposes only.**

**Darkryt Orbinautz presents...**

* * *

**Prologue**

Through out the realms of time and space, twisting in between parallel dimensional planes and rolling through the stars was a funny blue box.

Inside, the good Doctor, the Eleventh Doctor, rested on with his legs out and his arms crossed over the back of his chair. He was looking forward to a vacation retreat with his female counterpart, whom he would be meeting at their destination. As old and patient as he was, even the Doctor required a little rest and relaxation every now and then.

The box made a very distinct noise that sounded somewhat like a dry-heaving mechanical elephant with a breathing problem.

"Eh?" The Doctor questioned. It sounded like his TARDIS was changing course. He hadn't programmed it to do that. Snapping to attention, the Doctor spun his chair around and started pushing buttons and pulling levers. "Oi! That's not supposed to happen...stop that. Stop that this instant!"

The Doctor slammed a button, and got an obnoxious klaxon sound in response. The Doctor slacked against his chair in defeat. When that button gave a klaxon, it meant the TARDIS was going off on its own path, in spite of whatever The Doctor wanted it to do instead.

He knew his TARDIS. He knew it very, very well. He knew it wouldn't go off and defy him like this unless it had a good reason.

But it was still damn frustrating.

The Doctor got out of his seat and started rummaging through his cupboards and start just messing about with his things to pass the time while he waited for the TARDIS to finish its trip. Highlights included juggling bowling pins, wearing his fez- which WAS cool, by the way, no matter what anybody thinks- and holding an electric razor in his hand for a really long time. Why? Because he spent that long time wondering what he was doing with a razor in his cabinet. His chin didn't exactly sprout a squirrel's nest.

The Doctor stumbled when the TARDIS stopped moving, having reached its destination...wherever that was supposed to be.

Patting his jacket against his chest to make sure he looked pressed, he opened the TARDIS' doors, where he was greeted by an absolutely gorgeous ray of sunshine. Raising his arm to block the light, he stepped out to meet a most unusual sight.

He was on some sort of raised pavilion. In front of him were a gaggle of white unicorn stallions in gold armor, with a rather large mare of the same color standing in their center. Their leader, perhaps?

Having been (almost) everywhere, and having seen (almost) everything, The Doctor didn't find anything wrong about being greeted by unicorns. Or giant robots. But giant robots and unicorns together was a first, and there were two giant robots- one bulky and light green, the other swift-looking and silver- standing on the pavilion behind the gathered equines. They all shared in staring at him in surprised bewilderment.

"Huh." The Doctor remarked, putting his hands in pockets.

"Well, this is new."

* * *

_Well, I was sittin' 'round the table_

_What else had I to do?_

_That was when I_

_ looked up into the sky_

_And they called him Doctor Who!_

_Doctor Who is gonna fix it,_

_Doctor Who will make it right_

_A painted phone booth_

_of unsuspecting blue_

_But when inside the doors,_

_A vast internal complex_

_ Defies dimensional laws _

**Friendship Is Magic: Prime**

**Bonus Story**

**_THUNDERWING!_**

* * *

**ACT I: _Breakaway_  
**

The Doctor marched forward with his usual bravado, having on reason to be afraid of neither equine nor automaton, despite the fact that they both could trample him to death at a whim.

"'Ello." The Doctor greeted, waving his hand. "I'm the Doctor. You are...?"

One of the horses stepped forward. She was a big one, too. He had to look way up just to glimpse portions of her face. Or was it a he? Long lashes and curves like the ones in her face were generally feminine, but they certainly wouldn't be the first species he encountered where the guys were feminine and the girls were masculine.

The large majestic equine cleared her throat. "I am Princess Celestia of Equestria."

"Equestria." The Doctor repeated, clapping his hands and having a look around from the pavilion he was on. "Would that be this place?"

Celestia blinked. "What do you mean?"

"This place. This planet is Equestria?" The Doctor asked for classification.

Celestia nodded. "Yes. This planet is Equestria, and this is the city of Canterlot. I consider it the planet's capital."

"Ah! Wonderful. Planet's capital of a planet full of talking horses. Not that I mind. I speak horse, ya know. But then the horse speaks perfect English, it kinda takes the fun out of it for me. Say, maybe I do mind."

Celestia raised an eyebrow at the Doctor's rambling. Her muzzle curled into a bemused smirk, and she giggled. "I can tell you will be a most...amusing pony, Doctor."

"Pony? I'm not a pony, I'm a Time Lord." The Doctor replied. "Or is that a language thing?"

"It is, actually."

"Okay. Shouldn't take it personally, then." The Doctor muttered. He paced back and forth before stopping and pointing at the robots. "Say, what are those robots there?"

"Those are the Autobots Boulder and Smokescreen. They're here helping us set up a Space Bridge terminal for the use of pony civilians." Celestia put her hoof to her chin. "I'm sorry, do I need to explain Space Bridges to you, Doctor?"

"Nah, don't worry 'bout it." The Doctor waved a dismissive hand. "Space bridge. Bridge through space. What's there to explain, eh? Eh...wait." The Doctor's airy pacing suddenly turned brisk and rushed. "Did you say those two were...Autobots?"

"Yes...why, is that a problem?"

"No, no." The Doctor assured her. "At least, not with those two...don't think they recognize me." He muttered quietly.

"What was that?"

"Nothing."

"If you insist. Say, we never discussed what you were the doctor _of._" Celestia said with a intrigued eye.

The Doctor seemed taken aback by this. "Pardon? You're not going to say it?"

"...Say what?"

"You're not going to ask "Doctor Who?"

"Nnno...I thought you said you were just, 'The Doctor'."

"Well, yes, but that doesn't mean I don't like hearing it."

"Hearing what!?"

"Doctor Who!"

Celestia lowered her eyelids, steadily growing tired of The Doctor's and her's little word game. It was amusing, for a moment, but it had since ceased to be so. She wasn't a fan of the 'third base' antics.

"Answer my question, Doctor, before I send you on the tour with Smokescreen." She craned her neck towards the swift-looking Autobot.

"Mmm, fair enough." The Doctor nodded his head. "Doctor of, doctor of, what I am...the doctor of?" The Doctor curled his fist against his chin, then, in another moment displaying his eccentric eccentricity, moved his fist away from his chin, breathed on his palm, licked his palm, then dabbed his palm over his cheeks. "Hmmm. That's funny. Yesterday, my saliva felt like beeswax. Now, it's more like syrup. Anyways, let's say I'm The Doctor of...life, the universe, and everything."

Smokescreen winced, his hands arching back. "I'm not sure I want him to give him a ride with hands like that."

"Hmm? Oh, sorry." The Doctor reached his clean hand into his pocket and pulled out a hankie. "I've got some hand sanitizer in here somewhere..." He threw the hankie to the ground, then proceeded to pull out a variety of thing from his pocket in search of the sanitizer. Amongst them were a dog whistle, a rubber ducky, a rubber ducky with metal rings on it, a kazoo, and a blindbag pony figure of Celestia, of all things.

Celestia and a guard ducked their heads low to look it at the blindbag figurine after it fell on the ground. They exchanged confused glances.

"Here it is." The Doctor said at last, pulling some a generic 'germ blaster' and proceeding to wash his hand with it. "Hmm." After a moment's hesitance, The Doctor reached into his pocket again and pulled a short metal stick aligned with two rims at its tips.

Celestia wandered and leaned her head to inspect the curious device. "What do you have there, my good Doctor?"

"Sonic Screwdriver." The Doctor answered. "Helps me sonic things. Wanna see?" His question had a hint of pride in his tone. Celestia's curious expression was all the answer he needed. He pointed the Sonic Screwdriver at Celestia's horn, and it opened it at one tip to reveal a crystal inside. A high-pitched hum escaped from the crystal.

Celestia' dropped to her knees, grasping her horn in pain. The Doctor's eyes widened. Two guards rushed over the Princess' aid, one of which pointed a spear at him.

"What did you do to the Princess!?"

The Doctor raised his arms up in surrender. "I just...soniced her, is all."

"Well..." Celestia muttered, mustering up the strength to get back on her feet. "I must recommend you refrain from 'sonicing' anypony else on their horn...or wings. Or- actually, just to be safe, don't sonic anypony, at all."

The Guards helped Celestia walk away, off the pavilion and stepping onto the stairs that led down.

Smokescreen approached and crouched down before the Doctor. "Well, how about that tour?"

The Doctor paused for a moment and thought about it. "Sounds all right, then. Oh! Don't suppose there's any chance we could stop for muffins along the way? Feelin' a bit peckish."

Smokescreen blinked, confused, not having introduced to the concept of a muffin just yet. The rookie Autobot turned towards the Princess.

Celestia noticed over her shoulder. She nodded.

"I guess so!" Smokescreen said to the Doctor with a confused shrug. Pinching the scruff of the Doctor's coat with the tips of his fingers, Smokescreen jumped off the platform onto the grassy Canterlot grounds below, landing with a rather loud and hard thump.

"Smokescreen!" A medium-pitched voice exclaimed, somehow having the frame of mind to be scolding and not panicked. "Be more careful! You almost turned me into a pancake!"

The Doctor crossed his arms, swinging to and fro in Smokescreen's hands, unable to see who was talking to him.

"Oh, yeah. Right. Sorry, Twilight."

"It's fine...just don't let it happen again..." Twilight muttered.

Smokescreen converted into his swingin' ailen race-car vehicular mode, his hand lowering and dropping the Doctor gently as his arm folded into his body. The door to the passenger side shot open. "Hop in!"

"Yeah, just a mo'." The Doctor assured him, wobbling on the ground and attempting to gather his bearings. Twirling around, he came face-to-face with a lavender unicorn with purple hair. Despite not being allowed to use his Sonic Screwdriver on her, the Doctor got the distinct feeling something about this mare was...wrong, somehow.

The mare snorted at the sight of him and turned to leave.

The Doctor, unnerved by her curt dismissal walked to Smokescreen's side and brush his hand over the Autobot's hood. He pointed at the pony, wagging a finger at her. "Who is she, and why does she not seem to like me?"

"_Hmm? Oh, that's Twilight Sparkle._"

The Doctor stifled a chortle at the ridiculous naming of the ponies here. Celestia, Celestia he got. Celestia was a very old name, very...very powerful. But Twilight Sparkle? Sparkle!? Really?

"She doesn't like humans."

The Doctor made a derisive scoff. "Whaat? Rubbish! Pish-posh! Not like humans? What's not to like?"

"_Well, they're kinda soft and tiny and squishy-_"

The Doctor flexed his hand before giving Smokescreen a slap across the hood to keep him quiet, causing an echo of metal to ring out. "Ahhh, shaddup! I'm going to go set that _pony_ straight. Ah! Oh!" The Doctor walked briskly forward, coolly adjusting his jacket, before shaking his hand to relieve of pain. "Slapping an Autobot with the hand...not my greatest idea, no. Although, it's not quite as bad this one time where I tried to cross a toaster with a screwdriver..." The Doctor shook his head. He had to get to that pony. He flagged his hand out as he dashed towards her. "Excuse me! Excuse me, miss! Oi! Twilight Sparkle!"

Twilight stopped at the sound of her name. She turned her neck around, but was displeased to see the Doctor chasing after her.

The Doctor raced to her side and stood tall. "Right then, Twilight Sparkle?"

"Yes. What of it, human?" Twilight snapped at him rudely.

The Doctor flinched, taken aback by the absolutely staggering rudeness of the pony. He'd never met an unicorn so...ill-mannered before.

"First things first," The Doctor drawled in his light British accent. "First, I am not a human, I am a Time Lord. You hear me? Time Lord! Second, why so much hate for the human race, eh?"

Twilight sighed tiredly. "For one thing, all the humans I liked have betrayed my trust in one way or another, and second, one of their military commanders appears to have a personal grudge against me! Do you need anything more?"

"More would be nice." The Doctor absently answered, rocking his head. "Details are good."

"How about at least two of them have actively tried to kill me? On top of that, one _accidentally succeeded_ at killing me! I got better, though."

The Doctor pursed his lips. "Eh, yeah, okay. I can see how that might put a rain on your parade. But still! you can't hold the actions of three against an entire species!"

"Technically speaking, I can...since I _do._"

The Doctor squinted, mentally knocked about from Twilight's verbal uppercut. "Well, still..."

A car horn honked obnoxiously behind them. They turned to see Smokescreen's headlights serving as eyes staring at them. "_You comin', Doc?_"

The Doctor altered glances between Twilight and Smokescreen, in9decisive as to whether he wanted his tour, or wanted to slug it at with Twilight 'til she came 'round to her senses.

"Doc?...Oh my gosh, how could I be so stupid?" Twilight smacked herself in the side of the head. "Doc, Time Lord...I'm going to guess you also have a TARDIS?"

The Doctor was more than a little confused, and partially intrigued that Twilight knew about the TARDIS. "Yes. Why? What about it? What's wrong with having a TARDIS?"

"Okay." Twilight's breath shortened a little, like she was starting to panic, but also trying to keep calm. "This is going to sound crazy, but I was possessed by Unicron, A Cybertronian God of Chaos."

The Doctor nodded his head, motioning for her to continue.

"He could see inside my head and control my body, and I couldn't control his body, but I could see inside _his_ head."

The Doctor nodded again.

"Naturally, with him being an omnipotent god and all, there was a lot to see. One of things I saw was the Doctor, who I'm guessing is you, who had a tendency to appear just before a cataclysm."

The Doctor stared stoically for a moment. "You're right."

Twilight got on a beaming smile at being correct.

"That does sound crazy."

Twilight's smile sagged. How was she to know the Doctor disapproved of the notion of living, breathing gods?

Twilight turned around to leave, but Doctor held his hand out. "Twilight, wait." Twilight stopped and gave him an impatient glare.

"I can..." The Doctor paced back and forth in front of her. "Sense something..._off_ about you. What is it, if you don't mind me asking?"

Twilight heaved her head and sighed. "Hold out your Sonic Screwdriver."

"Oh. Oh." The Doctor shied away at Twilight's request. "The Princess said I couldn't use the Sonic on anypony..."

"You don't need to."

The Doctor was confused by this, but obliged, reaching into this pocket and pulling out his trademark screwdriver. Twilight raised a hoof and tenderly, tentatively, gingerly touch it to the screwdriver. A thin tendril of smoke waved out, and the Doctor could hear her flesh sizzling.

Twilight removed her hoof. "Are you sure you want to know?"

The Doctor nodded, putting his Screwdriver back in his pocket. Then Twilight said something that really caught him with his guard down.

"Do you believe, Doctor?"

He practically jumped backward as a violet and pink flames began to appear around Twilight's hooves. The flames flared up and began to enveloped her whole body. The fire flashed brightly before dissipating. When it was gone, violet crystal were poking out from various portions of Twilight's body, and a large set of bony, clay-like wings much larger than they needed to be lift her off the ground.

"I fly..." Twilight flexed her wing outward, showing how huge they were. They were bigger than Celestia's own! Although that was counter-balanced by a lack of substance between them, as they were quite bony. "On the wings of Unicron."

Twilight turned around and this time, there was nothing the Doctor could say to make her stay. Another whirl of purple fire encircled, and her mutations disappeared. She walked with her head low, clearly upset at having to show her not-so-secret to somepony whom she only just met.

"So, we still on for that tour, Doc?" Smokescreen asked.

"Yeah..." The Doctor muttered quietly, sobered by Twilight's dejection. "Be right along..." Never taking his eye off Twilight's direction, he walked back to Smokescreen, opened the car door and climbed in. Smokescreen backed in reverse before doing a U-turn.

* * *

Twilight trotted dejectedly on the streets, feeling saddened by the revelation of her 'secret'. She sighed again.

"I wish there was somepony else I could achieve symbiosis with...Shining Armor only does it when he has to, and while the Tracers are nice, they're not exactly great company."

Twilight stopped to think. "Hmm. Maybe I should give the Tracers stingers..." Tracers, though useful for teleporting organics, weren't much good in a fight against Cybertronians. They were distracting at worst, and a best, a swarm of them flying incessantly would make a bot panic...before they realized the Tracers had no bite or sting to go with them.

Suddenly, Twilight felt a pulse in her horn, feeling it light up, resonating with a signal of Dark Energon that was not hers...

Twilight looked around left and right, trying to find the source of the mystery symbiosis. Not that she was complaining, but in a way, it felt like she was exposing herself to a stranger. She noticed a pony in a traveling cloak that obscured their features, but she knew it was them.

They also knew it was her, as the instant Twilight saw her, the cloaked pony took off running.

"Wait!" Twilight shouted, holding her hoof. "Stop! I want to talk to you!"

Twilight gave chase, intent on not letting this potential symbiosis partner get away. She swerved around a sidewalk corner, and could see the tail end of their billowing cloak shortly before it slipped the next corner. Twilight continued her chase, and eventually found the cloaked stranger in an alleyway, resting. Probably thinking she had lost her pursuer.

"There you are!" Twilight declared, startling the stranger. As Twilight approached and cornered her, the stranger backed away, only to herself pressed against a wall.

Twilight put her hooves on the stranger's withers to pin her, then bit the hood and pulled if off, revealing...

"Trixie!?"

"Hello, Twilight Sparkle!" Trixie spat, unhappy to see her 'frenemy' in this state. "W-what brings you here in this dark alleyway?"

"I...followed you?"

"And Trixie was attempting to escape you. Funny, that." Trixie worked her sarcasm with a raised eyebrow.

"Why were you running away? I thought we were friends now!"

Trixie turned her head away. "Trixie... has a developed a problem. Trixie may or may not have thrown herself in with somepony she shouldn't have and been infected with an evil substance unrelated to the Alicorn Amulet. She also may have pleaded guilty for a reduced sentence."

Trixie pushed Twilight off and turned her head away. "Please, just leave Trixie alone to wallow in her misery."

Twilight chuckled. "Eh-heh...hehhehhehheh."

"What are you laughing about?" Trixie demanded harshly. She was in no mood for foalish games!

Twilight cupped Trixie's cheek and pulled the azure unicorn's head towards her.

"Please don't call it an infection. It hurts my feelings. It's really more of a condition."

Dark Energon surging through both their veins, Twilight touched her now glowing horn to Trixie's. Both unicorns' eyes flashed with the Dark color as an indescribable pleasant feelings of just being _connected _swelled in both of them.

"Y...you have Dark Energon in your system?" Trixie stammered. "You? Straight and narrow Twilight Sparkle?"

"It's a long story." Twilight said with a smile. "Say, I'm supposed to go visit my brother in the Crystal Empire later today, and he knows how much I love my friends. I'm sure he wouldn't mind me bringing a plus one."

Trixie's eyes got big and dewy. "What- not only are you inviting me to go meet your brother, who I'm sure is a very attractive stallion-"

"He's married."

"Oh. Hrmph. Oooh, never mind that! Not only are you inviting me to meet your family, but you're taking me to the _Crystal Em-pire!?_" The high note in her voice emphasized well Trixie's surprise and disbelief.

Twilight thought about this for a minute, stroking her own chin.

"Well, yeah! It's not that often you find a...symbiosis partner around here." Twilight said, blushing and shyly lifting her hoof.

Trixie returned the embarrassed, but pleasantly surprised smile.

* * *

The Doctor had his eyebrows furrowed and his fist pressed firmly into his hand as Smokescreen lazily rolled through town. The Time Lord was deep in thought, concerned over Twilight. How she, while thinking he was a human, so quickly dismissed him. How hurt she seemed when she had to reveal herself to him. Smokescreen eventually noticed.

"_You okay, Doc?_"

"Hmm? Yeah, yeah, just thinking, is all..." The Doctor assured him.

"_Oookay then._"

The Doctor continued thinking until he saw two white unicorns – one with blue hair, the other with pink- reaching over a counter to give what he had to assume was pony currency to a stall merchant, who gave them some fried doughnuts.

"Oi. What's this then? Stop right here." The Doctor instructed Smokescreen, intrigued by what he saw. "I'm interested now..." The Doctor made his way out of the Autobot and marched over to the stall.

"Howdy! What can I do fer ya?" The merchant manning the stall greeted. "Here for of Doughnut Joe's trademark doughnuts?"

"Eh, possibly." The Doctor shrugged. He was more interested in just observing the unicorns enjoying such filling jelly-filled pastries.

"Hm. Well, you've met Joe. I'm Fancypants, and this is my partner, Fleur-de-lise." The blue-maned unicorn introduced themselves. "Who might you be, my fine fellow?"

"The Doctor. I'm a Time Lord visiting from space."

Fancypants and Fleur-de-lise stared blankly at him.

"Right then." Fancypants shrugged the alarming revelation like shaking off a bug on his shoulder. "Are you finding Equestria to your liking, Doctor?"

"For the most part. I'm..." The Doctor paused, afraid what he was about to say would be construed as offensive. "I'm curious to see unicorns eating doughnuts. It's not all that common where I come from." He felt at ease around this Fancypants fellow, presumably because he had an accent not dissimilar to the Doctor's own.

Fancypants and Fleur chuckled at the Doctor's eagerness to see new and strange (to him) things. They bemusedly obliged his request and started to munch happily on their doughnuts, keeping the food in the air with their magic. The Doctor wasn't at all perturbed at this disruption of physics.

"Say, are those doughnuts any good?"

Fancypants' eyes widened. He cleared his throat and composed himself. "Er...yes. Pardon my suprise, Doctor. But these are the work of Doughnut Joe!" Fancypants gestured to Joe, who blushed at the compliment. "Of course they're good! Here." Fancypants used his magic to tear off a bit of the doughnut and levitated the bit towards the Doctor. "Try a bit before you 'ave a go."

The Doctor appreciatively took the doughnut-bit with a smile and observed it for a moment before putting it in his mouth. "Mmh! Say, these are good."

Fancypants grinned and chuckled. He pulled out a hoofful of bits from his pocket. "Joe, my good colt, a a half-dozen package for our friend the Doctor here."

"Comin' right up!" Joe announced proudly before ducking under the cover of his stall. There was a few pops from the counter, followed by a ding, and Joe resurfaced with a bag hanging from his teeth. "'Ere ya go!" Fancypants levitated the bag to the Doctor.

"Oh, you didn't have to do that!" The Doctor decried as the bag dropped into his hands.

"Perhaps not. However, consider this a polite gesture on my part." Fancypants bowed his neck. "To welcome you to Equestria." Fancypants and his companion took their leave. The Doctor turned and headed back to his ride.

"_Got a treat for yourself? Where's mine?_" Smokescreen joked.

"It was a gift." The Doctor responded, cleverly defeating Smokescreen's jab.

There was a beep-beep from Smokescreen's dashboard.

"_'Ey, Smokescreen!_" A sweet-sounding Southern voice came from Smokescreen's dashboard. "_Got sumthun of a situation 'ere back at the farm. Think y'all can head on over and help out a little?_"

"_Of course! Oh, but I have this, uh, sort of passenger?_"

"_Eh, bring 'im along. Could always use more hooves._"

"_All right! Consider me there!_" The commlink beeped off.

"Oi now. What's this then?" The Doctor demanded at the strange conversation to which he had absolutely no context.

"I guess I should explain. I kinda...have this thing going with these ponies called the Apple Family. They kinda take priority over you, so we're gonna head over to Ponyville."

"Oi now." The Doctor objected. "Celestia said you were supposed to be giving me a tour of Canterlot."

"Well, that's true." Smokescreen admitted.

The Doctor gave Smokescreen's dashboard a good solid thwack. "Oi! Just 'aving a bit of fun wit' ya. Let's go meet this Apple Family of yours, I'm sure the Princess won't mind! More, the merrier, I always say! Hahaha!"

"Well...if you say so!" Smokescreen, being young and inexperienced, took little to motivate him and even less to convincing. He revved his wheels (despite the fact he yet to get an Earth vehicle mode and hovered off the ground) and took off at blazing speeds, his motor running at its maximum. The Doctor dropped his doughnut bag and clenched his hands against the back of the chair, holding on for dear life as the insane speeds made his lips flap around wildly enough to reveal his gums.

* * *

After winding through more than a few suspended bridges and through a few forests, Smokescreen stopped at the outskirts of Ponyville, where a little-known entrance straight into Sweet Apple Orchards was placed that he traveled right through. He came to an abrupt stop, shaking the Doctor in his chair even more, and the unfortunate passenger was all too eager to get out of his ride. While Smokescreen converted to robot mode behind, the Doctor wobbled and clutched at his stomach.

The Doctor groaned in pain.

What was even worse was, in the high-speed ride that ensued, his doughnut bag was shaken and stirred until the doughnuts inside were nothing but paste adhering to the cardboard walls. However, it evened out, as he was going through too much motion sickness to even think about eating right now.

Smokescreen flexed his shoulders and twisted at his waist. "Ah! Feels good to exercise my hydraulics after being in vehicle mode for so long!"

"There y'all are!" The same sweet sounding voice from earlier called out. "Ah thought Ah heard the hum of a overripe engine!" A very orange pony with a cowboy hat trotted into view, followed by a group of other mares.

"Applejack!" Smokescreen shouted as a form of greeting.

"So, Smokescreen, y'all ready to get to work?" Applejack questioned.

"I'm always ready!" Smokescreen declared, punching his fists through the air to demonstrate his readiness. Applejack noticed the wobbling Doctor and got a concerned look on her face.

"Say, is yer buddy all right there?"

"Eh, he'll be fine."

"No!" The Doctor objected, raising his hand and barely keeping himself from throwing up. "I am most certainly not fine!"

"Hmm." Applejack pursed her lips. "Well, Ah can clearly see y'all are in no state to help buck apples...although..." Applejack turned silent, but it was clear from her expression she didn't think The Doctor had the muscle to help with the apples trees even if he was feeling well. She trotted towards him and lifted him up onto her strong back. "Here ya go. Sit there for a spell 'til you can stand up straight. Say, who are you, anyhoo?"

"I'm...the Doctor." The Doctor groaned out, lying on her back to gather his strength. Applejack ignored the weight on her back and proceeded on her work, walking up to an apple tree and bucking it untl the apples all fell off it onto the ground. As she worked, the Doctor noticed her friends and decided to strike conversation with them.

"So...who might you...all be?" The Doctor groaned on, rolling around on Applejack's back. He rather enjoyed and appreciated the feeling under his back. It was kinda like lying on a moving rock with a bed comforter on it. Though he didn't like the bump that rolled through Applejack's back -and by extension, his back- when she bucked the trees around.

"I'm Rainbow Dash, and these are our friends Pinkie Pie and Fluttershy!"

The Doctor raised his head up to see the three of them. He guessed the one with rainbow hair was Rainbow Dash, and the pink one was Pinkie Pie, so by process of elimination, that made the mutant one with swirling bronze patterns on green armor plating Fluttershy.

"Now hang on a sec, 'ere. What's with the cyborg pony?" The Doctor shook his head. "I don't believe this, a cyborg pegasus."

"Um..." Fluttershy mumbled. "Actually, I'm a techno-organic...there's a difference."

"Techno-organic, eh?" The Doctor exclaimed. "Oh, I want to Sonic you so badly..."

Fluttershy took a few steps backwards uncomfortably. "Um...that sounds inappropriate, Mister Doctor."

"Mister Doctor? Mister Doctor? You know, I rather like the sound of that!" The Doctor clapped his fists together. "Right then." He leaped off Applejack's back and climbed her down her side to the ground. He gave her a pat on the rump to show his thanks. "Thanks for being a bed for me, mate."

"No problem, sugercube." Applejack told him before continuing on her work.

"So..."The Doctor said, turning around. "Explain the, uh, explain the cyborg pegasus to me."

"Techno-organic." Fluttershy repeated quietly, though listening closely enough would detect a hint of irritation in her voice.

"Well, she, uh...kinda got converted. But it's okay. She likes it. Don't you, Fluttershy?" Rainbow Dash playfully banged a hoof against Fluttershy's armor. Fluttershy lived up to her name and nervously shied away from the attention.

"Well...a little." Fluttershy admitted. "I would never want to hurt somepony, but it's nice to know I don't have to worry about somepony beating me up."

Fluttershy was understating her own strength, as being part-Insection gave the parts of the Insecticons' incredible power.

"Fascinating!" The Doctor announced with a jerk of his head. He was familiar with the idea of an organic being cyber-converted...although this was a bit different from anything he was used to. "You know what would be great? If you could tell me more, eh!? Doesn't that sound grand?" The Doctor, trying to be friendly, cupped Fluttershy's cheeks. However, this startled her and made her convert into her ladybug mode involuntarily.

"Wha...she's not just a cyborg, but she's part Cybertronian!? Well, that is just- just- _cool!_"

"Yeah. She's still our Fluttershy, though." Rainbow Dash said, resting her knee on Fluttershy's beast-mode shell.

The group of ponies heard a the clop of two more ponies approach behind them, and they turned around to see Twilight and Trixie approaching.

"Trixie!?" All three mares exclaimed. "What are you doing here?"

"Trixie has discovered she has...more in common with Twilight Sparkle than she initially thought." Trixie answered.

Twilight narrowed her eyes at the Doctor and sneered. "Doctor, Doctor, why do I keep running into you?"

The Doctor shrugged cockily and walked towards them his usual irritating swagger. "I don't know. Why do you keep running into me?"

"I don't know, but I wish I'd stop." Twilight then ignored him for the rest of the conversation. "Anyways, Trixie and I are heading to the Crystal Empire to pay a visit to Shining Armor. We just wanted to inform everypony."

"All right then." Pinkie drawled.

"Have a nice time with Trixie and Shining Armor." Fluttershy said quietly.

"You sure it's a good idea to introduce her to your B.B.B.F.F?" Rainbow Dash asked with a suspicious eye towards Trixie.

Twilight glanced at Trixie worriedly, and Trixie glanced back sadly. Twilight hadn't at all thought about it like that...

"No, but...friendship is magic." Twilight answered, building her up confidence as she spoke. "Have a nice day, everypony!"

Twilight and Trixie turned to leave as everypony waved them off. The Doctor, meanwhile, rubbed his chin.

"I think I might like to see this...'Crystal Empire." The Doctor muttered. The gears in his head began grinding mischievously, and he rubbed his hands together. "So, Fluttershy the Cyborg, would you be up to help me hitch a ride?"

Fluttershy's beast-mode optic twitched. The Doctor, sensing an unforeseen volatility from the Insect/Pony, started backing away.

"TECH-NO-OR-GAN-IC!"

* * *

Twilight and Trixie boarded the Friendship Express, the train that would take them from Ponyville to the freezing cold Crystal Empire.

Behind them, Fluttershy skittered along the ground, the Doctor on her back, a little nervous about the Doctor's plan.

"Are you sure this is a good idea, Mister Doctor? It seems like we're stealing a free ride off the train..."

"Oh, fine." The Doctor sighed. "We'll pay them before going up. What do you ponies even use to pay for things, anyway?"

"Bits. Little gold coins." Fluttershy skittered up the train's cab and gave the conductor some bits from her insect leg. The conductor was nervous to take money from an over-sized metal ladybug, but upon taking them and seeing the coins were genuine, nodded them his permission for them to board.

Of course, when Fluttershy turned away from the train and flew up onto the top of a section, the conductor was a little baffled.

Fluttershy sunk the pointed tips of her bug legs into the cab, attaching herself into the cab.

Inside the cab, Twilight noticed six pointy things poking down from the ceiling of the cab she and Trixie were in. She looked to Trixie, who shrugged. Twilight turned and poked her head out of the window and was gobsmacked by the sight of the Doctor resting on top of Fluttershy, her wings held out to form a chair for him.

"For the love of pete..." Twilight muttered. "Fluttershy! What are you doing up there!?"

The train started moving. The churn and hum of engine forced Fluttershy to speak louder than she was comfortable, and Twilight to raise her shouting.

"The Doctor wanted to see the Crystal Empire!" Fluttershy shouted back. "He thought it sounded interesting!"

Twilight made a frustrated groan. "Quit following me, Doctor!...Why are you on the roof!?"

"Personal preference!" The Doctor shouted back.

"You prefer to be on the roof!?"

"Yeah! What's so wrong about that!?"

"It's just...strange." Twilight closed the window and sat back in her chair.

Nothing noticeably really happened on the way. When the grass turned to desert, and the desert then turned to snow, ice, and frosted over grass, The Doctor presumed they had to be getting close. He shivered and hugged himself.

"Are you cold?" Fluttershy asked.

"Am I cold? Yeah, I'm cold! Is the Crystal Empire this cold?"

"No."

"Whew! Well, that's a relief."

"It's colder."

"Bloody!"

The Doctor was starting to bitterly regret not going into the actual train. He was sure there was a heater, and maybe some hot chocolate there.

"Would you like huddle underneath me?" Fluttershy offered. "I'm sure my internal machinery will keep you warmer than just sitting there."

"Probably have a point." The Doctor admitted. He crawled off Fluttershy's back and wormed his way under her shell, where Fluttershy took her front two legs out of the cab and hugged him. Like she said, the heat from her machine parts was warmer than sitting on her back. Not by much, but it was something.

The Doctor noticed a pink flying thing off in the distance. "What's that?"

"What?"

"That pink flying there. Off in the distance." The Doctor pointed.

"Oh! I think that's Princess Cadence. She manages the Crystal Empire for Celestia...I wonder what she's doing out..."

* * *

Cadence flew along the Crystal skies, a basket hanging from her mouth. In the basket were some grapes, bananas and other fruits, as she was intending for a good day with Shining Armor.

As she was flying along on her way, she noticed a glacier. It was a humongous chuck of ice, but it was actually rather small for a glacier. She didn't think much of it, so she continued on her way, but her horn suddenly lit up and started dragging her towards the ice mountain. She tried to fight it and pull back on her way, but her horn dragged her down.

She sighed. She should have known better. When a unicorn's horn locks onto something and wants to investigate something, the unicorn had no hope of fighting.

Once she stopped resisting, she had a much smoother flight towards the glacier and she perched on top of a jagged ice chunk and scanned the area of the glacier. She really didn't see anything noticeable...

Until she swept her gaze over at the center of the glacier, and saw a humongous sword the size of Optimus Prime trapped inside the ice. It was beautiful, elegantly crafted and wonderfully sculpted. It was almost mesmerizing in its beauty.

"This must be one of the Iacon Artifacts Twilight's always trying to help Optimus find! I've got to tell her and Shining Armor about this!" Cadence realized. She flapped her wings and took off towards her original destination with a new sense of urgency. The existence of this sword had to be shared as soon as possible!

* * *

The Friendship Express pulled up into the Crystal Empire's train station. Everypony got off the train, Twilight and Trixie amongst them. Fluttershy bucked her legs out of the cab and hugged the Doctor to fly him off the train and onto the station. Hearing Fluttershy's wings, Twilight looked over her shoulder and glared at the Doctor. She humphed before continuing on her way.

"Oi. She does not like me, does she?" The Doctor remarked at Twilight's behavior.

"No...please forgive her. She has trust issues with humans."

"I'm not a human! I am a Time Lord!"

"Oh!" Fluttershy exclaimed, putting her legs over her mandibles in alarm. "I'm so sorry! I didn't know!...you still look like a human, though."

"No. No." The Doctor firmly insisted. "Humans look like Time Lords, not the other way around!"

"But you understand since you look like a human, Twilight's going to..." Fluttershy muttered. "Don't you?"

"Yeah, yeah. I guess. Hey..."

The Doctor noticed Twilight and Trixie trot up to a white stallion who had clearly been waiting for her.

"Twiley!"

"B.B.B.F.F!" Twilight exclaimed, running up to Shining Armor and engaging him in a hug. They wrapped their necks around each and nuzzled for awhile.

"It's good to see you again, kiddo!" Shining said, patting Twilight's shoulder and noticing Trixie. "Who's this?"

Twilight cleared her throat. "Sorry. This is my friend, Trixie."

Trixie's jaw dropped. "Trixie...I'm your friend, Twilight?"

"Well...yeah!"

Trixie's eyes wavered and blubbered. "Oh!" Overwhelmed with emotion, Trixie ran up to Twilight and gave her a hug.

"Okay, okay. That's enough. I'm getting too many hugs and Shining's not getting enough." Twilight said jokingly, lifting Trixie's leg off herself.

"Right..."

"So you're one of Twiley's friends, huh? A friend of hers is a friend of mine!" Shining welcomed Trixie with open arms, er, front legs, inviting her in for a hug.

Trixie approached, but when she stepped away from Twilight and towards Shining, putting herself in between them, all their horns suddenly burst into purple energy.

"Aaah!" Shining screamed, clutching at his horn in pain. "Twiley! What's...going on?"

"Uh, uh...symbiosis!" Twilight sputtered out. "Shining, I'm so sorry! Trixie has Dark Energon in her systems! I'm so sorry, I didn't realize-"

"That's why you wanted to Trixie to meet me!?" Shining demanded sharply, sounding enraged. "So we could all achieve symbiosis together!? As another partner for your damn addiction!"

Twilight made a sound like a sick duck quacking.

"I'm disappointed in you, Twiley." Shining said, turning around to leave.

Fluttershy and the Doctor stared with wide eyes. Twilight just dropped onto her haunches, unable to believe what she just heard.

Shining stopped. "Why don't you take some time and think about what you did?"

"Excuse you!?"

All eyes turned to Trixie, who was speaking now in the middle of this family confrontation.

"You think Twilight brought my here just to achieve symbiosis with you!? Don't flatter yourself!" Trixie snorted, puffing air out of her nose. "The Grrreat and Powerful Trixie would never want to achieve symbiosis with a such a quick-to-judge stuck-up unicorn like _you!_"

The hypocrisy was so thick it could've cut with a knife. And malleable enough a flat, not very sharp butter knife would do it, at that.

Now it was Shining's turn to have his jaw drop.

"Twilight brought Trixie here to introduce so we could all hang out together like good friends. You think she _likes_ the fact that she has to cope with this stuff?"

"Well, I..." Shining muttered at a half-attempt to salvage his pride.

"You think Twilight likes the fact she to go out and spread this infection of hers with other ponies just so that it doesn't kill her? You think she _likes_ being undead?"

"Well, that's actually come in useful at times..." Twilight mumbled, turning her violet eyes away.

"Why don't _you_ take some time and think about what _you_ did?" Trixie snarled. She wrapped her leg around Twilight's back and began to steer her away from the station like she was a protective boyfriend.

Shining just stood there, jaw agape, having to process so many emotions at once he couldn't even think of what he was supposed to do next- fairly obvious, "Apologize to Twilight" but in his current state, even so much as singing his A-B-C's was an impossible task.

"Well...I'm no expert, but I'm pretty sure that could've gone better." The Doctor silently quipped.

Cadence descended from the sky, making a bee-line for her husband. "Shining Armor! Where's Twilight? I've got something I need to share with both of you!"

"Don't bother." Shining bitterly spit before trotting off in the direction of the Crystal Castle.

Cadence raised an eyebrow, then noticed Fluttershy and the Doctor. "Hello! Uh, Fluttershy? Could you explain what's going on to me?"

"Well, basically, Twilight's broke up with Shining Armor to be with Trixie." The Doctor answered. "Does that help?"

Cadence stared.

"N...n-no, not really." Cadence's eyes started rolling around doing loop-de-loops in their sockets. "In matter of fact, I'm actually now even more confused."

* * *

Outside the city, Twilight sat on her haunches on the ledge of a bumpy part of the road, Trixie's leg wrapped around Twilight's neck. Twilight's had her hooves on her cheeks, wondering what she did wrong.

"I don't understand..." Twilight muttered. "I didn't mean for us to undergo symbiosis...why can't he see that?"

"Who knows?" Trixie said indignantly.

"...Trixie? T...th...t-thank you for standing up for me." Twilight stuttered.

"O-of course!" Trixie stuttered back, still getting the hang of this whole 'emotion' thing. "That is what friends are for, isn't it?"

Twilight gave a look of surprise. She smiled and gave Trixie a hug.

"I don't believe this." Twilight said. "I mean, doesn't he realize if I didn't use the Dark Energon on him, he'd still be dead!?"

Trixie patted Twilight on the back, content to let her rival just...vent and get everything out in the open.

"You don't need him." Trixie assured her.

"But I _do._ He's my _brother!_" Twilight countered.

Trixie frowned, unsure of how to proceed. "Well, uh...Trixie is sure he'll come around?"

Twilight pulled away from Trixie and sniffled. She wiped a tear from her eye. "You know what, Trixie?"

"Trixie does not know what. What?"

"You're right. Shining just has acceptance issues and he's taking it out on me. He'll apologize once he's had some time to think."

Twilight got up and began to trot out into the fields of ice and snow, standing tall and proud with the conviction this was just an unfortunate mishap, and not Shining's last words to her. Then, as if rob her of her victory, her horn suddenly giving off an intense light glare that made Trixie avert her eyes.

"Ooh...wow. Trixie, I'm getting an incredible feeling of symbiosis from somewhere! Come on, let's investigate it!" Twilight dashed out towards the fields, and her eyes turned the blank pink of a pony or 'bot deep in the thrall of Dark Energon. Trixie reluctantly followed, and almost immediately fell under the same spell.

* * *

The Doctor followed Fluttershy and Cadence as they attempted to track down Shining. Cadence had been fairly confident he was heading towards the castle.

"So, Fluttershy, can you explain this to me better than your doctor friend?"

"Well..." Fluttershy drawled. "Twilight was trying to introduce Shining to a new friend of hers named Trixie, and they all started to achieve symbiosis, so Shining got upset and snapped at Twilight, but then Trixie snapped back at Shining, and then all went they're separate ways."

"I see." Cadence said.

"I thought I heard Twilight say she didn't mean to and was sorry, too..." Fluttershy mumbled.

"Well, Shining's going to the castle to clear his head. We need to get there and talk to him so he knows what to do." Cadence explained.

Fluttershy came to a stop, and it took Cadence a moment to realize Fluttershy had stopped. "Problem, Fluttershy?"

"Yes...where's the Doctor?"

Fluttershy and Cadence looked left and right, as well as up and down, and Cadence saw the Doctor a few alleyways back, observing two Crystal ponies drinking from coconuts.

"Doctor?" Cadence spoke up. "Are you coming with us?"

"Hmm? Oh, right!" The Doctor turned and rushed forward to re-join them. "Sorry 'bout that. There's just so many unusual things around here. You know how it is."

"I'm not sure I do." Cadence muttered. "But to each their own."

The Doctor kept looking around, trying to find more new and interesting things. He was the Doctor! It was what he did, trying to see new...new...stuff.

They arrived at the castle, and the sight of Cadence made the Crystal serf ponies scramble to serve their princess, but Cadence held her hoof out for them to stop. She may have been a princess, but that didn't mean she liked being pampered. Not that she didn't, but she had more important things to do.

The Doctor was absolutely flabbergasted at the castle. "What is this place?"

"The Crystal Castle, the shining jewel of the Crystal Empire...pun not intended." Cadence answered. "It's been here for while. As long as the Crystal Empire has stood, so has it."

"Fascinating." The Doctor oohed. Every corner and staircase seemed to make him turn his head, every decoration seemed to enchant him, forcing Fluttershy to stop, turn around and poke him. There were so many things here! How was he supposed to take in it all?

"Shining Armor?" Cadence gently beckoned after they passed the fourth staircase. "Shining Armor, can you come out?"

Shining did so, though from the way he brutally flung the door open, it was clear he didn't want and wasn't in the mood to talk. "What?"

"I heard about Twilight and Trixie. What's going on?"

"What's going on, is that Twilight has a problem with Dark Energon and she expects me to be a part of it!" Shining flailed his legs about in his rage.

"Are you sure that's what happened?" Cadence softly asked. "It sounds to me like this is one big misunderstanding."

Shining frowned and looked away. "Maybe."

"There we go." Cadence said at Shining's admittance. "Maybe you should apologize?"

"Maybe..." Shining muttered, resting his head against the door frame. "...Yes."

"There we go, mate. Now buck up and go get on your knees and beg for forgiveness." The Doctor threw in his two cents, paying more attention to the surroundings than the conversation.

"Doctor, that's not helpful."

"Right. Sorry. I'll go over there." The Doctor pointed to a corner of the room. Cadence nodded, and he walked towards it. Cadence, however, didn't realize where the corner led.

The Doctor rounded the corner and saw something just as amazing as the sword Cadence saw earlier.

A huge crystal, beautifully and expertly carved into the shape of a heart, suspended between two icy pillars, floating and defying gravity, was visible through a window in the wall. It must've taken an artisan several hours to get this thing _just_ right.

"Wow." The Doctor whispered, putting his hands on the guard rail. "You are a beauty. What's your name?"

"That's the Crystal Heart."

The Doctor looked over his shoulder to see Cadence, Shining and Fluttershy approaching.

"It keeps the Crystal Empire safe, and tells Shining Armor and I how the ponies of the Empire are feeling."

"So like a mood ring, then." The Doctor joked.

Cadence chuckled at this idea. "Somewhat, yes."

The Doctor took in the serenity of the Heart. A serenity which was cut short by an urgent yell.

"Prince Shining Armor! Princess Cadence!" A Crystal Pony yelled, galloping up the stairs as if her life depended on it.

"What? What is it?"

The pony shuddered.

"King Sombra...is returning."

Cadence's, Shining Armor's and Fluttershy's jaws dropped.

"How?"

"That's impossible! The Crystal Heart destroyed him! Didn't it?"

"Apparently not!"

* * *

Meanwhile...several miles away from the castle. Several miles away from the Crystal Heart, and a very, very long trek away from any pony sensitive to Sombra's magic...

There was crater. A crater that had only just recently been made, as it was not there when Sombra made the Empire disappear. Nopony questioned much about, as they all thought the crater amidst the crystals and cliffs where it landed made for a beautiful scene. The towering white cliffs overlooking it gave an excellent perch to peer inside, but the crater was so dark and too deep for anypony to notice if there was anything inside.

There was a very large stack of crystals around the crater, completely covered in snow, obscuring their true appearance from anypony in viewing distance. They was something off about them, though. They were really quite pointed and jagged compare to the usual smooth round crystals of the Empire.

Two Crystal Ponies- one male, one female- were lying together and relaxing on the edge of one of the cliffs.

They were on each other, and there was no doubt they at least had some affectionate feelings for each other.

"Mmm, hmm." The male moaned, enjoying the female's touch.

"So, ready to take things a little further?" The girl questioned.

"Oh yeah!...Wait."

The female pouted at being told to wait. She had been waiting plenty enough already.

"Look." The male pointed at a cliff diametrically opposed to the one they were on. "Isn't that Twilight Sparkle?"

The female bolted upright, and saw that, yes, Twilight Sparkle, and Trixie, were overlooking the edge of the other cliff.

"It is!"

From the unnerving, vulture-like posture of the two unicorns, the Crystal mare knew. "Something's wrong."

Twilight quit staring at the gap and turned towards Trixie. "The horn, my faithful sssstudent." She hissed, clearly deep in the Dark Energon's thrall.

Trixie produced from her star-printed cloak...King Sombra's disembodied horn! Twilight took it into her hoof, then chucked over it over the edge where it fell into the pit.

The Crystal Ponies hugged each other, afraid of what was about to happen. They didn't know what it was, or what it was going to be, but they knew it couldn't have been good.

Seemingly, a pair of glowing green eyes with red, vertical snake-like slits with green mists flowing off them appeared in the crater. It was like the hellish eyes King Sombra himself had opened.

Then they closed, and a terrifying roar echoed out from the crater. With the roar came a flash of purple light that shone up. A ring of purple energy rose up from the crater and tore through the snow around, revealing the crystals present to be, in fact, Dark Energon.

A gigantic claw reached from the crater, and grabbed the crystals for support. With a deep groan of effort, wings appeared from the crater, and the demonic beast dragging its way out of Pony Hell appeared burst forth in a display of power, its wings beating proudly and irritably.

It was a huge monster, somewhere between Bruticus and Trypticon in size. It looked like someone had taken a Decepticon, and a demon from human myth, and smashed the two together until they merged into one. Then they put a the coat of a Crystal Pony on the result. The wings were large, and oddly-soft looking, with a pattern like a computer grid running through them.

The beast flexed its barn-sized wings.

"Is...is this some reincarnated form of King Sombra?" The mare squeaked out, noticing the demon had Sombra's eyes and thinking this may have been a long-reaching plan of Sombra's in the event of his demise.

The two stood there and huddled against each other, not expecting an answer.

"**No.**" The demon roared. His voice carried all the destructive intent of a Decepticons's, but without the passion and pleasure Decepticons had for it. Like destruction wasn't a passion for him, but a required programmed motion he was predetermined to engage in.

He slammed his bus-sized fist into the edge of the cliff they were on, making it shake and rattle beneath their hooves.

"**I am Thunderwing.**"

* * *

**Author's Notes for "Breakaway"**

**So, I was going to delay posting this until I had Act II set up, but I noticed it was prime-time for maximum story views on a weekend, and I sometimes need some reassurance from reviews, so Act I is up early.**

**I was going to complete the second act and just cast it as one large big story originally, but then the above happened. This is _entirely legitimate_ for a first chapter, and it's just..._sitting around_ in my documents, doing _absolutely nothing._ It's upsetting!  
**

**Had it remained the one-shot it was going to be, there would be no chapter titles (hence the Acts.) **

**Chapter Title Meaning: taken from an obscure Autobot, "Breakaway" refers to Shining Armor and Twilight having their argument, how Trixie takes Twilight away from Shining (...er, only in a _physical_ sense, of course!) and the _break-_ing of Thunderwing from his crater.**

**So, how do you like the story so far? **

**Oh yes, before I forget, this is, along with "Up In Smoke" part of the "Infiltration Lead-Up." Which is...*gasp!* _leading up_...to a new story...called *gasp!* _Infiltration. Never would've_ figured that out on your own, would you?**

**_/Sarcasm  
_**

**Oh, um...I used the Eleventh Doctor because I couldn't decide between whether to use the Tenth, Eleventh, or Doctor Whooves. Whooves felt like 'chickening out' so I wouldn't have to _choose_ one to me. In the end, I went with the Eleventh, because he was the _current_ one at the time of writing. (I used the same logic to make my crossover use _Transformers: Prime)_**


	2. Dark Envoy

**Transformers and My Little Pony are the properties of Hasbro.**

**Doctor Who and related concepts are the properties of The BBC broadcasting network.**

**This is a non-profit work made by an independent contractor outside of ****any**** company's official notice intended for non-profit entertainment and speculative purposes only.**

**Darkryt Orbinautz presents...**

* * *

**Friendship Is Magic: Prime**

**Bonus Story**

**_THUNDERWING!_**

* * *

**Act II : Dark Envoy  
**

The Doctor clapped his hands, noticing the tension and air of dread in the room. "Right-o! King Sombra, probably derived from Portuguese for 'Shadow'..."

Cadence's eyebrows shot up. "You speak Portuguese?"

"And 699 other languages, including horse, baby, Arthurian English, pig, and spider." The Doctor boasted.

Cadence put her hoof on her chin. "Sound the alarm. Get every defense you can set up."

The Crystal mare nodded and ran off, on her way to bellow out through the streets King Sombra's dreadful encroaching.

"Shining, I'm going to cast a force field on the city. You get to the main entrance and help set up defenses, then come help me." Cadence ordered.

"Right!" Shining nodded. They ran off to resume their positions.

"So, Fluttershy." The Doctor said, breezily walking along at his own pace, showing no fear in the face of danger. "Explain to me this King Sombra chap."

"He's an evil unicorn who enslaved the Crystal Ponies. We all thought the magic of the Crystal heart killed him, but apparently not..."

The Doctor clapped his hands. "Sounds like a jolly good time! I, er, don't suppose you'd be up for taking to the front gate, eh?"

Fluttershy converted to lady-bug mode. "Hop on."

The Doctor jumped, clapping his feet together in obvious excitement. Once he climbed onto Fluttershy's back and positioned himself, he whistled with enthusiasm. "Off we go!"

With Fluttershy's Insecticon-level of flight, it took no time to fly the Doctor from the castle to the front wall of the Empire and for them to land on the terrace, where a mixture of Crystal guards and Shining's own soldiers were scrambling to set up the first line of defense. Shining's men were rolling cannons into position, while the Crystals were waving funny sticks and muttering, casting enchantments on stone unicorn heads.

A shadow approached from behind them. The Doctor looked his shoulder to see a sparkling light blue dome forming over the entirety of the city.

"Everything ready!?" Shining bellowed from atop a command tower.

"Ready, sir!" The Guards below saluted.

The Doctor looked around and hmmed.

"Is something wrong, Mister Doctor?"

"Oh, nothing. Just don't like the looks of this...I've got bad experience with the military."

"Well, I'm sure Shining Armor and the Crystal Ponies would never hurt anypony if they could avoid it..." Fluttershy scraped one of her six legs.

Every solider around remained tense, looking stoically on the horizon, their eyes fixed like hawks. Serfs were constantly running up the stairs, dropping bags of gunpowder for the soldiers' use. Shining took a long sweep around the area before turning to descend from his outpost and assist Cadence.

"Sir!" One of the Guards shouted, pointing. "Twilight Sparkle is approaching!"

"Twiley!?" Shining darted down the terrace, and sure enough, Twilight and Trixie were runnnig towards the main gate at unusually fast pace, like something was chasing them.

"Twiley!" Shining screamed, putting his hooves around his mouth to increase his volume. "I'm sorry about what I said! I just...I just can't handle being all Dark Energon-y and I took it out on you!"

Twilight kept approaching, like she hadn't heard a thing Shining said.

Shining's lips quivered, thinking Twilight was ignoring him out of spite. However, as she got closer, Shining noticed something alarming. "Aww, scrap."

"What?" The Doctor inquired.

Shining pointed. "Look closely, Doc."

The Doctor squinted his eyes. Proving unable to make out anything, he rounds his hands around his eyes like binoculars. Shining turned to Fluttershy for an explanation of the Doctor's bizarre behavior. Fluttershy shrugged.

"Yeah?" The Doctor asked, not seeing what was wrong.

"Can you see that pupil-less, pink stare in her eyes?"

"Uh-huh. Eeyup." The Doctor nodded slowly, wondering where this was going.

"That means she's undergoing deep symbiosis. In other words, I could apologize at the top of my lungs, wearing the most ridiculous, humiliating outfit I can think of, playing the smallest violin in Equestria with tears in my eyes...and she wouldn't care."

"Okay." The Doctor said, taking his 'binoculars' off. "Sounds like a problem."

"You have no idea."

Twilight and Trixie abruptly stopped, some distance ahead of the force-field.

"Why are they stopping?" Fluttershy wondered. "They know we'll let them in...don't they?"

Twilight's and Trixie's mouths opened wide. Purple energy began gathering and swirling around their lips. The energy coalesced into balls, and the unicorns let out huge blasts at the force-field.

Shining was stunned, Fluttershy was panicked, and the Doctor was mildly amused.

"Since when does Twiley have a _mouth laser!?_"

"It's really more a of a _laser breath_ than a mouth laser..." Fluttershy mumbled incoherently.

"Presumably, they learned from that strapping young fellow." The Doctor said, pointing upwards.

"What?" Shining exclaimed. He and the guards looked upwards, and they were all horrified at the sight.

Thunderwing's truly gargantuan form came flying overhead. He flexed his wings and 'stood' proudly in the air. Everypony immediately noticed how he seemed to have Sombra's eyes.

"What is that thing!?" Shining yelped.

"Well, based on the pointy bits, I'd say it's a Decepticon." A solider with a scar under his eye answered. "Not that you would know that."

Shining glanced at the scarred guard.

"Pardon me if I was there helplessly watching the Princess surrendered her crown to the Decepticon Lord while you were off getting your horn licked by the Changeling Queen!"

Shining stared even more dumb-founded.

"Yes, I'm _bitter!_"

"OI!" The Doctor snapped his fingers. "Knock that off. Now's not the time to picking up on grudges. We should see what this 'Decepticon' wants..."

Whether or not Thunderwing heard the Doctor was unclear, but he gave an answer nonetheless.

"**I am Thunderwing! Surrender the Matrix and go unharmed!**"

"Matrix!?" Shining screamed. "What's he talking about, a Matrix?"

"Um..." Fluttershy muttered. "The Matrix of Leadership is, um...kinda like the, uh...Optimus Prime's 'crown'? It says he's a Prime, and it's kinda like the Elements of Harmony..."

"So, it's complicated?" The Doctor interjected.

"Oh yes. Very."

"Splendid!" The Doctor clapped his hands. "I love complicated things! Don't you?" Shining just stared.

Thunderwing flexed his wings again and began charging up. The same thing that happened to Twilight's mouth happened to his, and he let loose another blast against the force-field. It really was more a laser breath, kinda like a high-tech fire breath. It only helped to draw the comparisons between Thunderwing and a demon.

Inside the castle, Cadence shivered, her horn feeling the brutal attack. The beam of light connecting her horn to the force-field wavered and shimmered as she struggled to keep her shielding up.

"Stay here!" Shining ordered. "I'm off to go help Cadence!"

Shining ran down the stairs as fast he could.

Thunderwing's keen, hunting optic noticed the pony running away from the gates towards the castle, and his instincts told him that the pony had to be stopped. Aiming his arm-cannon, he fired a huge purple sphere of energy that hit against the force-field harshly and began to distort the reality around.

The Doctor, feeling the rip in dimensions, winced and clutched at his two hearts.

The blast phase-shifted through the force-field and passed through, where it landed on the ground behind Shining. The explosions sent Shining flying through the air and tumbling on the ground.

Thunderwing and the two enthralled unicorns prepared more breaths of lasers. Shining's men scrambled to improve defenses before the fast-approaching onslaught fired, but their efforts for nought and in vain. The lasers-breaths trailed along the ground before raising up against the force-field. Thunderwing's own laser-breath was powerful enough on its own, but Twilight's and Trixie's help, it took no time at all to start cracking the shield.

Cadence stumbled, unwilling to give up defense of the Crystal Ponies under her care. But Thunderwing was starting to overpower her magic...

"Shining, where are you?" Cadence questioned out loud. A tear rolled down her eye. "I need you..."

Thunderwing fired another blast, and that was it for Cadence. The force-field shattered, and the pink Princess collapsed to her knees.

Seeing the protective bubble popped, the Crystal Ponies abandoned all pretenses of bravery and ran for shelter. They hid themselves in their homes, in their closets, stuffing themselves and their foals into cupboards, if not taking a deep breath and diving into the nearest pond. None of the Crystal Ponies wanted to give much thought as to how Thunderwing's skin became so much like their own. Fluttershy grabbed the Doctor and pinned him under her shell to keep him out of Thunderwing's sight.

The cannons and enchanted unicorn statues began firing at Thunderwing, but their attempts were laughable. Even Thunderwing was hard to miss, their shots seem to bounce right off his hide. The 'Decepticon' flew over the gate and briskly landed in the Empire's street, his wings folding up into rather swank fins on his back.

The Doctor peeked his out head out to observe the situation, and saw Thunderwing walking through the streets with tension, like he was looking for something. The Doctor pushed Fluttershy's shell up like a rock and sped out from under her.

"Doctor? Doctor, what are you doing!?"

"I'm gonna go do what I do best!" The Doctor answered, giving her a reassuring hand signal.

"Which is!?"

"What do you think!? I'm the Doctor! Think, Fluttershy; what does a doctor do?" The Doctor riddleed her before running down the flight of stairs, his coat billowing behind him impressively.

Fluttershy converted back to her pony mode. "...They fix things!" She realized after the Doctor was out of her sigh.

"'Just a 50-foot Decepticon walking through a pony town. Don't mind me none'." The Doctor joked to himself as he walked quickly towards Thunderwing's imposing shadow. He whistled for the giant's attention. "'Ey! Thunderwing! Stop right there!"

Thunderwing did indeed stop, but when he turned around, he met the Doctor with aggression. "**Who dares to give me orders!?**"

"Ah, that wasn't an order, that was a request." The Doctor cleverly remarked. Thunderwing rolled his optics and huffed.

"Now, I've got a couple of questions, if you don't mind? What are you doing here on Equestria?"

"**I was created by my master, Unicron, to seek out and destroy the Matrix of Leadership." Thunderwing answered. "I was dormant, sealed inside a meteor until it crashed on this world and entombed me in the ice! I was reactivated a few hours ago, and I am here, now,**" Thunderwing pointed at the Crystal Castle. "**To remove the Matrix from that tower and destroy it at last.**"

"Matrix isn't in there, mate."

Thunderwing narrowed his eyes. "**I sense its taint. BAH!**" Thunderwing roared arching his claws and flexing his wings. "**The more I talk to you, the less I can fulfill my mission!**" Thunderwing flapped his wings and flew towards the Castle. The Doctor ran under Thunderwing's off the ground feet and headed to get to the Castle first. He was barely able to reach the entrance before Thunderwing's shadow fell over the towers.

The Doctor dashed in and looked around. The Crystal Ponies were all huddle into corners, their front legs over their eyes. The Doctor noticed Cadence at the top of the stairs, struggling to get up. He ran up the stairs and knelt by her side.

"Doctor..." Cadence grunted, out of energy. She tried to get up, but collasped. She tried again, but seeing that she wasn't going to get up anytime soon, she let her body go limp. "Don't...let Sombra get the Crystal Heart."

"It's not Sombra, mate." The Doctor told her, giving her a relaxing stroke through her mane. "But I'll still stop for you, sweetheart."

Seeing the Doctor rush up another staircase towards the Heart, with a such a stark seriousness and trained determination after such a flirtatious way of addressing her Cadence chuckled.

The Doctor's footsteps echoed off the stairs and around the walls as he raced to reach the Heart first. "How long are these stairs? They weren't this bloody long when I was here earlier! I mean, for Celestia's sake..."

After much tedious stair climbing, The Doctor finally reached the chamber where the Crystal Heart floated. The Heart's rate of revolving had slowed since he last saw it, as well...

"O-kay!" The Doctor clapped his hands and rubbed them together. "Got to the Crysteal Heart first, right. Now what I'm going to do about?" The Doctor picked at his teeth like a piece of brocili was stuck in it. "Plan. I need a plan." He started pacing. "Come on, come on, come on..." The Doctor held his hands out like he was doing a magic trick. "Plan!"

There was a moment of awkward silence.

The Doctor sighed and put his fingers over his mouth. "Okay. No plan. Well.."

Whatever train of thought the Doctor was about to go off on, it was interrupted by the sound of Thunderwing's wings flapping. "Ooh...balderdash."

As Thunderwing's form descended near the side of the castle, the Doctor skidded backwards to come face-to-face with the demon. Thunderwing's eyes were gazing intently on the Crystal Heart, claw outstretched to snatcth the relic.

The Doctor eventually noticed how Thunderwing was hesitating. "Well, that's odd." The Doctor chuckled and put his arms on the guard rail. "Not what you were expecting, eh?"

The Doctor didn't realize just how right he was. In that exact moment, fresh scans of the Crystal Heart from multiple angles were bearing compared and contrasted against old files of the Matrix's appearance in Thunderwing's vision. When a "NO MATCH" had been confirmed, Thunderwing drew back his claw and unfurled his wings. He jumped into the air.

"**Though holy, this artifact is not the Matrix. My sensors have led me astray!" He jumped into the air. "Come, my servants!**"

He flew over the Crystal Empire's walls while outside, Twilight picked Trixie up and began to fly away.

Shining weakly looked up at the sight of his flying sister. He raised a hoof for her attention. "Twiley..."

For a moment, Twilight stopped and turned around to look at him...but then her horn shimmered purple, and she continued on her way. Defeated, Shining collapsed back down on the bejeweled pavement.

"Hmm." The Doctor tilted his head in confusion, wondering why Thunderwing hadn't taken the Heart. Sure, he mentioned it wasn't the Matrix, but surely he would've been able to find some use for it, wouldn't he?

"I mean, that is what bad guys do, isn't it?" The Doctor asked himself.

"Doctor!" Cadence exclaimed, rushing towards the Heart's altar.

"You're looking better, Cadence."

"The Crystal Heart! Did he take it?"

"Nope." The Doctor pointed to the Heart, where it was slowly returning to its original fast pace.

Cadence stared, as confused now as she was worried before. "What do you mean...are you going to tell _he just left!?_"

"Yep. That sounds about right."

Cadence turned to stare at the Crystal Heart with a gaping, shocked mouth. "Why would he leave it alone?"

The Doctor shrugged. "Beats me. Maybe he has a fashion complex."

Cadence sighed and shook her head.

Fluttershy came fluttering up the stairs with Shining Armor on her back, and she gently laid him on the ground before Cadence. Cadence rushed to comfort her mate.

"Cadence..." Shining said, weakly lifting his head up before turning downwards in shame. "I'm sorry...I should have been able to get to you in time."

Cadence smiled kindly, and kissed him on the forehead. "It's not your fault." Cadence shuddered. "Whatever that...thing was, he was powerful."

Shining closed his eyes. "This is all my fault. Twiley went and brought that thing online because she was upset about what I said."

The Doctor clapped his hands for attention. The sound echoed off the walls, making it a fairly successful gambit.

"Don't talk like that, Captain." The Doctor began marching back and forth, carrying an aura of authority and power from himself as he did so. "Let's recap. What do we know for certain?"

"Shining Armor and Twilight had a spat." Fluttershy provided.

"That whatever that thing is, it somehow sends off King Sombra's energy." Cadence added. "And that he doesn't want the Crystal Heart."

"You say Sombra was killed. You haven't mentioned to me how."

"Well, the Crystal Heart shattered him into a billion pieces."

"All right, I want you to do something for me, Cadence." The Doctor said slowly, tilting his head. "I want to imagine...that Twilight Sparkle and Trixie, combed over every last inch of the ground..." The Doctor wiggled his fingers downwards, meant to convey a sweeping motion. "And picked up all those pieces, and then used them to activate Thunderwing."

Shining seemed surprised. "That thing has a name?"

"Yeah, of course." The Doctor answered dismissively. "Loads of things you can do with a name. Names have power..." Shining whinnied in disbelief, but the Doctor turned upwards with a smile, reminiscing on his past victories. "I am The Doctor...that phrase. That phrase alone has brought whole armies to their knees."

"All right then. What did your fancy magical phrase do to Thunderwing?" Shining asked, which broke the Doctor's thunder somewhat.

"...Don't know." The Doctor answered, not realizing he hadn't introduced himself to Thunderwing when he had the chance. "I'll have to check. I'll be sure to let you know."

The Doctor rubbed his chin and slowly turned around, realization dawning upon him. "He said the Crystal Heart wasn't the Matrix. Fluttershy, would you say that the Crystal Heart has anything- anything all- in common with the Matrix?"

Fluttershy nodded. "Oh yes! Most definitely!"

"So, bear that in mind..." The Doctor muttered, looking down as he thought to himself. "What's Thunderwing's next move?"

"He's...probably going to Canterlot after the Elements of Harmony!" Fluttershy exclaimed.

"Oh no, not_ Canterlot!_" The Doctor groaned, thowing his hands to his sides. "That's where I left the TARDIS. Agh! I hate it when the bad guys go after the TARDIS!"

"I'm sure Celestia is taking good care of your belongings." Cadence attempted to assure him.

"How do you know?"

"The Princess is a kind and caring individual who takes her responsibility to be hospitable to her guests seriously.."

"Right." The Doctor soldiered on and thought for a second. "Elements of Harmony...what are those, exactly?"

"Doctor." Shining interrupted, having regained the strength to stand. "I need to apologize to my sister. I want Twiley back."

The Doctor turned silent, and unlike before, the effect his silence had on the room was quite noticeable. He, taking care to emphasis the sounds of every step, walked up to Shining and held the unicorn's face. "Now you listen here, mate. I...will get your sister back. That's a promise. You hear me? A promise."

"What if you can't?"

"Aahh, rubbish!" The Doctor twirled around away from Shining. "I'm the Doctor. There is nothing I can't do!"

Cadence gazed on wistfully. "You know...for awhile there, I thought you were a silly man with a funny blue box. But seeing you promise Shining Armor something like that...tells me you're so much more."

The Doctor turned to Cadence and glared furiously.

"Now listen 'ere, you." The Doctor growled, approaching Cadence, causing the Princess to back away. "Let's one thing, and one thing straight right here. Always remember, and don't forget- don't you dare forget...because it may have irrevocable consequences on your life"

The Doctor halted his advance, and his expression turned into a wry smile.

"I _am_ a silly man with a funny blue box."

The Doctor turned back 'round to his crowd of Fluttershy and Shining Armor, putting his hands on his hips.

"Now, which of you three..." He said, pointing to each of them in turn. "Is going to give me a ride while we track down Thunderwing?"

Shining and Fluttershy looked at each other, then back to the Doctor, smiling at his enthusiasm. Said enthusiasm was somewhat infectious after it reached a certain point.

* * *

"******I sense its power. Its radiance. ********I know the Matrix was on this world once, even if it is not now!**" Thunderwing growled as he flapped his wings over the Crystal skies, Twilight flying underneath him. Crystal Ponies throughout the land were shuddering at the feeling of Sombra's magic returning, then turned to see with relief that it wasn't him. Only to scream and hide at the sight of this really quite amazingly huge flying demon.

Thunderwing's steadfast wing flaps suddenly slowed, and the demon clutched at his side like he had stomach cramp from swimming in water after eating.

"******My time in the crater has made my body adopt the coat of the natives...**" Thunderwing reflected.** "********Significantly weakening me! Servants!****" **Thunderwing roared and turned around, wings flaring out as he did so. "******Come! Back to the crater where you found me. I must recharge.**"

Twilight silently nodded, and changed course along with her master, Trixie still hanging from her hooves.

Thunderwing did not know nor did he care why these ponies had rebuilt him. He just knew that made for good servants while in their thrall.

* * *

The huge, cold doors of the Crystal Empire's imposing gate opened with all the furious speed of a drunk snail. Out came Cadence, Shining Armor, and the Doctor atop Fluttershy's back, riding off into the cold, wintry veil of the Crystal Empire's vast plains.

"So cold. So bloody cold. WHY is it so bloody cold!?"

"Because..." Cadence started to answer. "I don't know." Cadence looked to Shining.

"Don't look at me!"

They quickly rode out to find and defend the Crystal Empire against Thunderwing. Their shared hope was that maybe a passing traveler, perhaps a merchant, had seen Thunderwing on his way and could point them in his direction. They did not have to get far from the gate to get their first helpful hint, though it wasn't the one they were hoping for.

Shining Armor's horn suddenly formed a deep, bright sphere of purple light at its tip. All three horses came grinding to a screeching halt.

"What is it?"

"My horn is..." Shining grunted. "Detecting a cluster of Dark Energon."

"Is it big?"

"_Massive._"

"Right! Let's go check it out, then, eh?" The Doctor adjusted himself on Fluttershy's back. "Yeesh, your armor plating is uncomfortable in your pony mode..."

Fluttershy apologized to the Doctor for something she had little to no control over. Shining Armor got on to her for doing so. Cadence yelled at them both to knock it off so they could go investigate the Dark Energon, and maybe, just maybe, find a trace of Thunderwing.

With Shining's horn somewhat literally lighting the way, it took no time at all for them to reach the crater Thunderwing had been imprisoned. There, they saw the humongous surplus supply of Dark Energon pointing out and poking every which way.

Cadence and Shining Armor were shocked and horrified for different reasons that there was so much Dark Energon so near to an area they had been assigned to protect.

Shining whimpered and shuddered, feeling the increasing urge for symbiosis in his horn. "So much...Dark Energon."

"H-how did it get here?" Cadence wondered, her eye turning watery as she mentally berated herself for failing the Crystal Empire.

"Don't know." The Doctor said, hopping off Fluttershy's back and readying his Sonic Screwdriver, which whirred and hummed in a fairly ominous fashion. "I do know how it's getting out of here, though, haha! With a little help from my Sonic-"

The group heard the loud flap of large wings overhead.

"Or not!" The Doctor exclaimed, recognizing the sound as Thunderwing. "Hide! Get to cover!"

The group scrambled and ran around in circles for a little while before they all ducked down behind some snow piles, their heads barely peaking out over the frozen rain.

Thunderwing and his slaves came flying into view. Thunderwing slowed his wings and descended briskly into the crater, resting himself against a wall of cold rock. Twilight dropped Trixie off on the cliff-side next to him and descended herself.

Areas of Thunderwing's armored shoulders began shifting around, clicking and whirring as they converted. Panels split open to reveal a spherical, rimmed, ringed thing inside his shoulders- one each.

"Those look like engines..." Shining whispered.

The Doctor disagreed. "Look more like reactors to me."

"Quiet!" Cadence snapped. "Something's happening..."

Twilight's and Trixie's horns began to shimmer and shine. Shining's horn joined in, flaring up brightly, longing to join them, but Shining slapped it, preferring being unable to use magic over succumbing to symbiosis.

Thin narrow beams shot out from each of the two mares' horns that connected and tied themselves to the generators in Thunderwing's shoulders. Thunderwing let out a relieved sigh.

"**Yes...yes! Symbiosis!**" Thunderwing flexed his wings and raised his fists in the air before slamming the later down on the clifftops. "**I feel my power returning!**" He began to shake and sway as cracks appeared in skin.

"Look." Cadence instructed. "What's happening to his skin?"

The coat of Crystal continued to crack, and eventually, it began to peel off in the form of flakes and fall, leaving huge pieces of useless Crystal husk on the ground while also exposing some of Thunderwing's true colors; literally. There was some white revealed on his arm, some green on his thighs and chest, and some purple on his right wing.

"**Yes!**" Thunderwing cried out. "**Some more of this, and I will be free of this Crystal..._inhibitor!_**"

Some flawed logic in that, as Thunderwing's having a Crystal Pony coat was the result- not the cause- of his strength fading while slumbering in the crater. But try telling him that.

Cadence rose up from her hiding place bravely, a determined expression on her face. "We have to stop him. There's no need for him to gain any more power."

"I can't hurt Twiley!" Shining objected.

"But you already did..." Fluttershy pointed out.

"When!?" Shining snapped, unable to believe he would lay a hoof on his sister.

"...When you snapped at her bringing Trixie along for symbiosis, even though that wasn't true?"

"Oh... yeah. Right. That."

The Doctor stepped out of his hiding place and glared Thunderwing down.

"Doctor, what are you doing?"

"I have a plan." The Doctor answered mysteriously. He pointed quite emphatically at them. "Stay here, you lot." He began walking up the curved slopes of the cliff, intent on confronting Thunderwing directly. As if on cue, a high sharp wind began blowing.

"Hey! You! Big one up there!"

Thunderwing immediately got off his resting place and turned to glare back at the Doctor.

"You may not know me..." The Doctor shouted, frigid cold winds blowing his hair and coat around and turning his sweat into ice. "But we met in the Crystal City! I forgot to introduce mysef, but I am-"

"The Doctor!" Thunderwing answered.

The Doctor tsked, then turned around to Shining Armor. "Well, there you go, Captain. Are you satisfied!?"

"I thought you looked familiar, so I scanned my databanks, and yes...you have changed, but you are still the Doctor, Slayer of Daleks, Enemy of the Cyberiad, Last of the Time Lords." Thunderwing narrowed his eyes and leaned forward.

"So tell me, what do you hope to do against a being such as I?"

The Doctor stood expressionlessly, showing no sigh of letting the cold wind around affect him adversely in any shape or manner.

"I intend...to fix things." The Doctor said with a smirk.

Running up the hillslide, the Doctor leaped over a bump, striding through the air with all the grace of a pegasus (who was small, short, and hadn't learned to fly), landing flat on his face just before Twilight's and Trixie's hooves.

The Doctor lifted his head from the snow, spitting snowballs out from his mouth. "Pfft! Pto! Anyhoo..." The Doctor pushed himself upwards, lost his balanace on the slippery cave slide and took a moment to regain his footing. After that, he pulled out his Sonic Screwdriver.

"The Princess told me not to do this again...but I think she'll make an exception, don't you?"

The Doctor slammed down on the Screwdriver's toggle switch, activating it, and swept it over both Twilight's and Trixie's horns.

"Aaah!" The two mares both exclaime in pain, rubbing their horns sorely while the distinguishing characteristics of their eyes- pupils, irises- returned.

"Doctor!" Twilight growled upon reopening her eyelids. "What are you..." Trixie poked Twilight in the shoulder to get her attention. Looking up before she could really lay into the Doctor, she noticed Thunderwing. "What...is that!?"

"Mm. I'd say it's a twenty-story tall Decepticon, who's rather bent out of shape he can't find and destroy the Matrix." The Doctor remarked.

"I know not these Decepticons, but I am not one!" Thunderwing protested.

"Yeah? Well, listen here, buster;" The Doctor boasted, walking towards Thunderwing with no detectable trace of fear. "You just lose your two unicorns. What are you going to do now?"

"An unfortunate...but acceptable loss. Nothing will keep me from my mission of destroying the Matrix!" Thunderwing roared and yet again flexed out his wings, his Crystal coat cracking and peeling even more in the process.

"He's gaining power!" Twilight somewhat obviously exclaimed.

"Yes. We know that, Twilight. Thanks for the hint!" The Doctor yelled.

"I'm sorry, Doctor, but-"

"OH FOR PRIMUS'S SAKE!" Fluttershy screamed from her hiding place. "WOULD YOU TWO GET A ROOM!?"

The Doctor blushed profusely while Twilight stared confusedly. "I don't know what that means."

"Trust me, Twilight...you don't want to."

"WRRAAH!" Before the Doctor and Twilight could resume their argument, Thunderwing aimed his arm-cannon and fired. Twilight, Trixie, and the Doctor just barely ducked out of the way in time. The blast hit the snow they were previously occupying, and said snow went flying everywhere, giving Twilight, Trixie, and the Doctor all fines coats of the white powdery stuff.

"Come on! Again?" The Doctor protested.

"Come on, Twiley!" Shining yelped, rushing to his sister's side with horn ablaze and giving a hoof to help her up. "We can take him!"

"No, we can't!" Twilight objected.

"That's quitter talk!"

"No, really, Shining. My, Trixie's, and your magic all have traces of Dark Energon in it! Any spell we use on him will just make him heal and gain more strength!"

Shining made an expression of exasperation at being unable to do_ anything _to help combat this looming threat to them all. "Well, then what _can_ we do?"

"We can think of a plan!" The Doctor shouted.

"Twilight Sparkle, Trixie." The Doctor said with a steely seriousness. "You rebuilt him. _You_ let loose that thing on the world. _How?_"

Twilight put a hoof on her head, trying to remember what she did while under the thrall of symbiosis.

Thunderwing began charging his arm-cannon and fired at them, sending Trixie, Twilight and the Doctor all flying in different directions. The displaced snow spray from the explosion began giving them all nice white coats of the powdery stuff.

"Oh, not again..." The Doctor grumbled at being send face-first into the ground a second time. He felt his way around and began to roll over. "I don't suppose that blast did anything to jar your memory, Twilight?"

"Yes, actually!" Twilight answered as they all got up. "We found King Sombra's horn!"

"Great! Now what we do about it?" Shining exclaimed, following up with a groan.

"The horn is inside Thunderwing's power-core link." Twilight explained, knowing from her symbiosis the exact details of Thunderwing's creation...his specs, his schematics. "If we can get inside and remove the horn, it should disable him."

The Doctor rubbed his hands together. "Let's do that, then, shall we? How do we get in?"

Twilight pointed at Thunderwing's still-sparkling chest, where open slits in his armor were visible through his crystal coat. "Those vents there are small enough we could get in."

The Doctor took a moment to regard the vents, considering their validity as entryway's into Thunderwing's gigantic systems.

"Mh. Okay. Yes. Eeeyup." The Doctor pointed to Cadence and Fluttershy. "Princess! Fluttershy! We need your help! Get over here and fly me up into one those holes in Thunderwing's chest."

Cadence and Flutteshy didn't seem to understand what the Doctor was intending to do, but they obliged his request, coming out of their hiding places.

"Why are you going in? I know his schematics!" Twilight exclaimed, her voice carrying perhaps just a little bit of actual...concern for the Doctor.

"I'll figure it out. I'm clever like that, you see." The Doctor poked the side of his to prove his boast. "That's me. The Clever Doctor."

Twilight didn't appear too convinced by this, but she relented. "Fluttershy, fly with Cadence and bring the Doctor into those ridges -you see 'em?- and keep your commlink open so I can guide you through. Trixie, Shining Armor and I will keep Thunderwing distracted so you can get in."

Fluttershy nodded before converting to ladybug mode. The Doctor spread his arms out so Fluttershy could lift him up. Fluttershy and Cadence began flying up towards Thunderwing. Thunderwing wasn't blindly obvious, however, and began firing a rapid barrage of shots from his cannon.

"**Get out of my way! I will destroy the Matrix, and you shall not stop me!**"

Fluttershy and Cadence split away from each other and began to fly around to avoid Thunderwing's barrage. Thunderwing refused to let up on his assault, firing blast after blast at them. It was almost like he knew what they were up to and was intent on not giving them the opening they would need to slip in.

Twilight squinted, narrowing her eyes as she formulated an intensely complex battle plan that would distract Thunderwing. What they needed was to keep his attention scattered and unfocused, too much for him to aim reliably on a single target... Twilight already having been something of a stragist even before joining the Autotobts, she had no trouble figuring what to do."

"Shining Armor, Trixie, start running around in circles around the crater. Strafe your fire on him, shoot at him, but do not hit him. Remember; our goal is to distract him so Fluttershy can fly the Doctor inside. Got it?"

Shining and Trixie nodded affirmatively.

"Good! Now_ quit standing there_ looking at me for orders and _roll out!_"

Shining and Trixie attempted to gallop away in opposite directions, but they were so close to each other that their noses collided painfully against the that of the others. For a proud Captain of the Guard like Shining, this was mildly embarrassing. For a arrogant, haughty, stuck-up magician like Trixie, it was downright humiliating.

Even worse, Cadence caught sight of it and took it the wrong way, thinking of them had been trying to flirt with the other and making a reminder in her head to grill them both about it. A shot from Thunderwing's cannon that narrowly avoided clipping her wings completely removed the thought from her mind though, so Shining was off the hook.

After righting themselves and taking a moment to make sure their trajectiores wouldn't crash into each other, Shining Armor and Trixie began running around the crater, firing laser blast from their horns, taking care that would actually miss Thunderwing. (Which was kinda hard to do, since Thunderwing was so huge.)

One of Trixie's shots, though, hit the side of Thunderwing's face, cracking the coat and turning the eye of Sombra back into the orignall, empty black, fan-blade red optic of Thunderwing's orignal form.

"Trixie!" Twilight scolded.

"Sorry! Trixie missed! ...Wait, Trixie is supposed to miss, so wouldn't that be that Trixie hit...?"

"Never mind! Keep shooting around him- not at him!"

The trio of unicorns continued their shots, attempting to keep Thunderwing's fire spread around the area. When he made an ill-content roar and fired both his arm-cannons in opposite directions, Twilight knew her plan was going to work.

"Um, Doctor?" Fluttershy spoke quietly. "Do you mind if I use my beast-mode cannon?"

"That depends...how much recoil does it have?"

"A little."

Before the Doctor could ask how little was a little, Fluttershy unfurled her conical laser from between her mandibles and fired a shot at Thunderwing's shoulder. It was a good shot and made Thunderwing jerk, but its lasting effect was minimal.

The Doctor shook his head, the recoil from Fluttershy's weapon going through her legs and into the shoulders she was holding him by. "Okay. So that's how much is a little. Good to know for any future adventure we have."

Thunderwing was distracted from the direct hit on him, and quit firing at Trixie and Shining. He relaxed his arms like taking in a deep breath as he prepared his laser breath. Fluttershy ducked downward to avoid the blast, which disoriented the Doctor somewhat. The laser flew off into the distance.

"We got him switching targets!" Twilight yelled to Shining and Trixie. "Maintain fire!"

Cadence, inspired by Flutteshy's direct hit, fired off a few rounds from her own horn, which...somewhat dinged Thunderwing slightly on some of the more pointier bits of his armor.

Thunderwing's head swiveled around as he attempted to keep track of who was firing at him, and from where.

Growling ferociously, Thunderwing crossed his arms and attempted to fire at Shining and Trixie at the same time, though they each managed to jump to the side to avoid.

Seeing their opening, Fluttershy and Cadence blazed forward at Thunderwing's chest, full steam ahead. The Doctor grimaced and braced himself for impact. His entire vision went dark as Fluttershy entered into the black, cavernous ridge...

* * *

The Doctor blinked a few times, trying to regain his vision after they successfully infiltrated Thunderwing's internals. Thunderwing's insides weren't exactly what the Doctor or Fluttershy were expecting. The Doctor was expecting something more like that of a regular Cybertronian. Cadence was more thinking something along the lines of fire and brimstone.

Instead, however, Thunderwing's insides were like a great, big huge steampunk machine, bronzed-over copper coating every piece of heavy, grinding whirring machinery, gears spinning and levers pulling crazily. From the shape of the clear tubes and pipes around, it was meant to carry Dark Energon from one part of Thunderwing to another, like circulating blood. But instead of liquid Blood of Unicron, there was instead green magic of King Sombra's horn traveling through the pipes.

Fluttershy gently sat the Doctor down on the ground before landing herself, Cadence descending gracefully behind them.

Fluttershy pushed a button on her leg. "Twilight, we're in. Now what?"

"Find Thunderwing's power core! Sombra's horn will be floating in the air."

"Locate power core, disable floating horn." The Doctor summarized, more for his own benefit than anyone's.

Cadence idly looked around the room for clues, but she let out a tiny gasp too quiet to be heard. The Doctor and Fluttershy didn't notice, it was so hushed, but they heard the horrifcalyl high-pitched metal shriek and solid thump of Cadence's body against the wall. They turned to see Cadence pinned against a large piece of machinery by some black, purple-accented beast, which noticed them staring.

"What is that thing!?" The Doctor exclaimed.

"Unicronian Anti-body!" Fluttershy answered, eyes going bug-eyed (pun not intended.) "And if there's one, there's probably be more..."

"Well, I suggest we start running before they show up!" The Doctor turned to run away, but Fluttershy gripped him by the arm and held him there.

"No. Autobots never leave a mare behind!"

The Doctor raised an eyebrow, differences in Autobot and pony language causing Fluttershy's exclamation of the mantra to not give its intended message.

The Anti-body, as though obliging Fluttershy, shrieked again and charged at Fluttershy and the Doctor. The Doctor ducked down, sliding on the floor, but Fluttershy converted to beast-mode and scissored the Anti-body's neck with her mandibles, and began to apply pressure to her mandibles to crush said neck.

The Anti-body began shooting off yellow sparks, flailing and trashing about as Fluttershy pinched it, until finally its rune lines quit glowing, and its body relaxed, landing on Fluttershy's underbelly. The Insecti-pony-con pushed the body off herself and rolled back onto her feet.

"Thanks for the save..." Cadence muttered, rubbing her throat to be sure she could still breath.

"What was that?" The Doctor shouted at the gruesome display of violence.

"Sorry. Autobots are taught to fight, not run."

"Yes, well, Doctors- like_ me_, for instance!- are taught to run, not fight, and avoid violence whenever possible." The Doctor griped, standing and brushing his coat off.

"You think you could've reasoned with it?" Fluttershy asked with a hint of healthy skepticism.

The Doctor looked at the dead Anti-body's corpse, which still looked intimidating even in death.

"...No."

Another Anti-body came shrieking into view and body-slammed itself right on top of Fluttershy, pushing her body to the ground. Cadence, returning the favor, blasted the Anti-body off with her magic. While the Anti-body shifted around and righted itself, Fluttershy jumped on top of it, shoved her hoof/clamp into it, and tore out its circuity.

"Bloody 'ell!" The Doctor swore. "That's _violent_!"

"Sorry..." Fluttershy mumbled, oddly apologetic for this one even though she didn't seem bothered by her brutal takedown of the other. "Insecticon instincts..."

"We need a new plan." The Doctor concluded. "You two stay here and deal with the Anti-bodies. I will go and find the power-core link."

Another Anti-body came flying right at the Doctor's back, and he was only saved by Fluttershy's and Cadence being quick on the draw.

"Okay." The Doctor said, shaking his head at the third, smoking corpse in the room.

"Better plan; we go find the link together, and guard you from any more Anti-bodies that are waiting." Fluttershy suggested. "And, um...please trust me when I say that there is _probably more waiting._"

* * *

Outside, Twilight, Trixie, and Shining Armor continued to fire misamed laser blasts at Thunderwing, though Shining's military training led to him aiming 'correctly' and hitting Thunderwing in the shoulder, powering Thunderwing's ancient engines with the Spark of Unicron again. "**Grah! Is this the best you can do!?**"

"Shining!" Twilight berated him.

"I can't help it! I'm a military officer! I'm trained to exercise precise aim!"

"Hmm." Twilight grunted, annoyed. Using her magic to disappear and reappear as Thunderwing attemped to crush beneath his fist, Twilight noticed Thunderwing was still hovering over the crater they had found him in.

"...Trixie?" Twilight said quietly to her student.

"Yes?"

"Take note;" Twilight raised her hoof. "The Doctor, Fluttershy, and Cadence are inside Thunderwing and are about to deactivate him."

"Yes..." Trixie nodded, confused at why Twilight seemed so displeased.

"He's flying over the pit...that's full of Dark Energon...which, if he's deactivated, he will fall right back into it."

Trixie looked upwards as she gave this some thought. "Well, that's bad, isn't it? Wouldn't he just recharge and come back more powerful?"

Twilight giggled and gave Trixie a playful bop on the cheek. "You've learned well! Stay here and cover fire with Shining for me while I go get the Crystal Heart."

Twilight turned and ran off, teleporting as she ran to avoid Thunderwing's energy blasts.

"You're leaving us to fight this thing alone!?" Shining exclaimed at her departure.

"Yeah, don't think this means you don't have to apologize to her!" Trixie snapped at him.

"What- NO! I ALREADY DID THAT!"

"Trixie didn't hear you say anything of the sort..." Trixie said in her usual dismissive tone.

"You were enthralled in Dark Energon!"

"All the more reason you should apologize to your sister!"

"I- where's the logic in that!?"

* * *

The Doctor kept having to duck so much to keep his head from getting ripped off by an Anti-body, and drop down to the floor to let Cadence and Fluttershy shoot their respective lasers, the Time Lord though he was going to need back surgery when they were done.

"How big is this Decepticon?" Cadence balked.

"You think this is big?" Fluttershy responded. "We should take you to the New York Bay to see Trypticon's body sometime..."

"Trypticon?" The Doctor asked, balancing out on the grates composing the floor. "What's a Trypti-COOON!"

The Doctor fell down off the edge of the grates they were on, just barely managing to grab his hand precariously on the ledge of the steel.

"Doctor!" Cadence exclaimed, rushing to the edge with Fluttershy. "Are you all right?"

"I'm fine, girls!" The Doctor assured them, looking down. Even though the best advice for him would be not to look down. "Although, I think I found Sombra's horn!"

Fluttershy and Cadence extended their equine necks over the ledge to look down, and they saw it- King Sombra's curved, red horn sitting misplaced inside a cluster of Dark Energon that was curly and gnarled even for Dark Energon inside a futuristic furnace, visible through a door with ventilation holes. There was small ring of roosts around the furnace. They were probably used by the Anti-bodies to perch on and use their thin tendrils to perform maintenance on Thunderwing.

The Doctor climbed back up onto the platform they were on, backed away and bent his knees. Swinging his arms to and fro, he got ready to spring off. "I'm gonna jump!"

"Wha- there's no need to jump!"

"Nonsense, Princess!" The Doctor scoffed as he dashed across the platform, He jumped off the edge, his coat billowing out behind, and just narrowly caught his hands on one of the roosts. "Ah-ha! Yes!"

"Doctor, you're with two ponies who can fly." Cadence growled at him, annoyed.

"...Oh...right."

"There was no need to jump!"

The Doctor, ignoring Cadence's lecture about safety, swung from roost to roost, climbing them like monkey bars. He reached up and pulled open the door easily. Cadence thought it was actually rather too easy. Her thoughts were entirely justified when a large swarm of Anti-bodies came flying out of the woodwork – er, metalwork? Whatever. The Doctor made haste and crawled inside, crawling over the Dark Energon spikes in an effort to get to the horn.

Cadence and Fluttershy stared the swarm down, not intimidated by their superior numbers and fired their weapons. They hit some Anti-bodies in the optics, blinding them and preventing them from being major threats, but they were so many of them that they kept coming. One of them got close and managed to whip Cadence in the face but good with its tendril. She punched it in the face before it could strike again.

"Doctor!" Cadence yelped. "Are you okay?"

"I – am – walking -across – crystals...of pure evil!" The Doctor grunted out, reaching from one tip of Dark Energon to the next. "That is...generally..." The Doctor lost his footing, kicking off a small piece of Dark Energon that fell down and bounced on the other, lower parts of the cluster, making clinks that echoed with every bounce that were not reassuring. "Not...in... my definition...of okay!"

"Well, try to hurry it up!" Cadence shrieked as she pounded another Anti-body. "Fluttershy and I can't hold these things off forever, Doctor!"

"Hang on, hang on..." The Doctor muttered at her, reaching up higher and pulling out his Sonic Screwdriver.

An Anti-body wrapped charged right at Cadence and wrapped its tentacles around her neck. Cadence starrted grappling with it, trying to use her hooves to pry the tendrils off. "Doctor!"

"I'm trying! Cover your ears!""

"DOCTOR!"

Doctor adjusted the setting on Sonic by pushing a button. The tip of it opened, revealing the green crystal inside.

"DOCTOR!"

With a heavy grunt of rage, the Doctor aimed the Sonic Screwdriver at Sombra's horn. The Screwdriver let out a sonic pulse that hurt Cadence's, Fluttershy's, and even the Anti-bodies' ears. The Anti-body with its tendrils around Cadence let go and dropped to the floor.

"Right! Got it!" The Doctor reached up and jerked the horn from the crystal depositit. "Oh! Ow! Evil evil evil evil!" The Doctor bounced the horn around in his hands like a game of hot tomato before he raised his Screwdriver and soniced it again, rendering it dormant so he could shove it into his pocket and figure out what to do with it later.

Cadence turned around with an elated smile on her face. "Doctor, you did it!"

"Yay!" Fluttershy said quietly.

"Well... I _am _the Doctor, after all." The Doctor replied smugly, resting his shoulders on the Dark Energon spikes. Cadence shook her head at his eccentricity.

There was a loud groan and grumble, followed by a thud. It didn't take much to deduce the thud was from Thunderwing clutching his stomach in confusion.

"**What's...happening to me!?**" Thunderwing exclaimed. The loud metal groans were accompanied by everything around them shifting.

"Why don't we get out of here?" Cadence politely suggested.

"Sounds good to me, Princess!" The Doctor answered. Cadence lifted him into the air with her magic and placed him on her back. She and Fluttershy then turned around and galloped back the way they came, building up speed before they made a running jump to take flight.

Trails of leftover blue magic and orange energy trailed behind Cadence and Fluttershy as they appeared, rushing out of Thunderwing's ventilation.

"Cadence!" Shining exclaimed, waving his hoof for her attention. "You're okay!"

Cadence just smiled at him.

Behind them, Thunderwing's comatose body made a loud rumble as it feel into the crater, knocking up snow and whipping it into a cloud like an explosion.

"YEAH!" Shining cheered, jumping and raising his hoof into the air. "We beat him!"

"Everypony stand back!"

Everypony turned around, and except for Trixie, were confused to see Twilight Sparkle running towards the crater with the Crystal Heart floating on her back.

"Twiley?" Shining questioned. Twilight ran by him, completely ignoring him. Not out of resentment or malice, but simply from being too focused on her task. "What are you doing?...You're going to give that thing the Crystal Heart, are you!?"

Twilight stopped to glare back at him. "Yes, Shining, I'm going to give Thunderwing the Crystal Heart."

"Twiley! You can't do that! I know you're upset about what I said earlier, but-"

"This isn't about what you said earlier! This is about-"

"**RRAAH!**"

Thunderwing came flying out of the crater. Every last piece of Crystal Pony coat on him cracked, shattered, and fell away, fulling revealing his true form of a large white and green robot, his golden face, and his purple wings. His entire body was engulfed in an aura of Dark Energon, purple fires encasing him, swirling around his limbs.

"**I AM THUNDERWING!**" Thunderwing proclaimed to them. He raised his claw and made a fist at all of them. "**Now, feel the full, raw, power of SYMBIOSIS!**"

Twilight, Shining, and Trixie all grunted when they were engulfed in the same Dark Energon aura, made to unwillingly achieve symbiosis with Thunderwing. Eyes burning brightly, they all collapsed and fell onto their sides.

"No!" Cadence exclaimed.

"**YES!**" Thunderwing replied without really thinking about it, flapping his way out of the crater towards them. His shoulder panels unfolded, revealing the generators inside them again. "**I will destroy you all, and then I will find the Matrix!**"

Cadence and the Doctor started backing away. The Doctor noticed, out the corner of his eye, the Crystal Heart still floating above Twilight's body. He looked at it, then to Thunderwing. He bumped his elbow into Cadence's knee.

"Princess, I think I know what Twilight was trying to do." The Doctor whispered to her. "We need to get him away from the crater. Do you understand?"

Cadence nodded.

"Good. Think you can, uh, distract him while I get the Crystal Heart?"

"I'll try." Cadence answered. She trotted towards Thunderwing, which made Thunderwing pause, as he was confused why she would suddenly come forward for her doom at his hands. "Hey! Thunderwing! Has anypony ever told you, uh, you, uh..." Cadence rubbed her chin, not sure what to call him that he would actually find insulting.

The Doctor tip-toed cautiously towards the Crystal Heart, trying really hard not to catch Thunderwing's attention.

"Uh...uh..." Cadence continued to stutter. Thunderwing turned his attention away from her, no longer amused by her stuttering, and he noticed the Doctor.

"**What are you doing?**" Thunderwing flew up and towards up, but Cadence flew up as well and put herself in Thunderwing's way.

"If you want him, you have to through me." Cadence growled at him.

Thunderwing pointed his cannon at her. "**With pleasure!**"

The Doctor grabbed the Crystal Heart, discovering to his dismay that it was actually kind of heavy for somepony like him that didn't have magic to make it float above him naturally.

Cadence flew away from the crater, barely Thunderwing's laser fire or clawed grabs at her tail. "Come on, Doctor!"

"Right!"

The Doctor ran as fast he could with the Heart weighing him down, following after Cadence's trail in the sky and hoping Thunderwing wouldn't realize their plot and turn around to shoot him instead.

"Right..." Wind whipping her hair into her face, Cadence glared out of the corner of her to gauge how close the crater was to them. Not far enough, so she kept flying. The Doctor kept running as well, and he was really starting to wonder when they would stop, as his legs were getting tired and he soon wouldn't be able to run anymore.

Cadence made another check for distance, and decided they were far enough. She turned around to face Thunderwing again. "All right, Doctor, now!"

The Doctor stopped, spun in place to build momentum, and tossed the Heart into the air. Cadence caught with her magic, and before Thunderwing realized what was happening, Cadence hurled the Heart into the ventilation shaft she had entered and exited out of.

"**No!**" Thunderwing tried to block it with his hand, but his reaction was just a split-second too late, and ultimately, there was nothing he could do. Thunderwing clenched his claws in pain while Cadence grinned at her victory. Thunderwing dropped to the ground and stumbled on his talons. "**I feel...cold. No! I AM THUNDERWING! I AM THE DARK ENVOY!**" Thunderwing's chest shifted, revealing a generator just like the ones in his shoulders, though larger. "**If I must expend every ounce of energy in my core to defeat you, then so...be...it...**"

The generator in his chest began glowing blue, when it probably was meant to glow purple. Thunderwing's red eyes also turned into blue, the Crystal Heart's energies flowing through him in place of his natural Dark Energon powers. Blue light shot from his eyes and his mouth. He clutched his head in pain. "**No! NO!**"

Cadence and the Doctor raised their respective appendages to block the huge flash of light from the Crystal Heart as it flashed brilliantly, tearing Thunderwing apart from the inside out. When the light had gone, Thunderwing was lying on the ground, his body burnt black and smoldering, the Crystal Heart rotating above him triumphantly.

Now with their source of their overload gone, Shining Armor, Twilight, and Trixie came to, rubbing their heads sorely. Shining quickly noticed Thunderwing and the state of his body.

"..._Huh._ He shrunk."

"The Crystal Heart made him shrink." Twilight concluded. "At least the Empire is safe now...until the next threat comes along."

Shining glanced at the ground uncomfortbly.

"What's wrong, B.B.B.F.F? We won!"

"I'm sorry!" Shining abruptly yelled at her. "I'm sorry for all those rude, horrible, mean things I said to you at the train station earlier, and I-"

"Shining..." Twilight put a hoof to her brother's mouth. "I forgave you for that hours ago. I just wasn't sure if- if you forgave me."

"Aww...come here, little sis!"

Shining and Twilight engaged in a hug.

"Well..." The Doctor said proudly, watching the siblings hug as Cadence landed beside him. "Now that's a happy ending, don't you think, Princess?"

"It sure is, Doctor." Cadence agreed. Even Trixie seemed to have her heart warmed. She was looking away from everypony and dabbing a tear out of her eye while her mouth made little coo's.

* * *

******Epilogue: **

"So, Doctor," Shining asked as he walked the good Doctor back to his TARDIS. "Will you visit Equestria again?"

"Well, I'm certainly not making any plans for it..." The Doctor answered as he swung the TARDIS' door open. "Then again, I never make plans for any of my visits, so who knows? ...What's that?"

A loud metal tromp distracted Shining and the Doctor from their talk of plans. They turned to see Optimus and Celestia approaching.

"Is-is that Optimus Prime?" The Doctor asked...rather fearfully.

"Yeah. Celestia thought it would be good to introduce to you to each other."

"Oh, well, that's really not nessecary, Shining. Optimus and I already know each other."

"Oh!" Shining perked up. "So you're like old friends?"

"Uh, no. More like a war criminal on Cybertron."

Shining stepped backwards, blindsided. "I-I'm sorry, how are you a-"

"Time traveling ailen, big misunderstandings. No time to explain, maybe later!" The Doctor told him quickly, retreating inside the TARDIS and piloting it to disappear just as Optimus and Celestia arrived.

Shining cleared his throat and tried to pretend nothing was wrong. "Hello, Optimus. Hello, Princess."

"Hello, Captain." Celestia greeted, looking around for the TARDIS. "Where's The Doctor?" She didn't notice Shining trying to cue her not to say the Doctor's name.

"The Doctor?" Optimus inquried. "As in...the last of the Time Lords?"

Shining knew better than to try and con Optimus. "...Yeah, that's the one."

Optimus' expression grew displeased. "You are aware of what the Doctor has done to Cybertron in the past, during the period of the War for Cybertron?"

"...No?"

Optimus made a displeased grunt. "Mmm."

"..._Should_ I know?" Shining asked innocently.

"No, but I will you regardless. Once, there was an artifact of intense power, called the Underbase. The Decepticons and Autobots agreed not to use for their goals, as it would cause too much destruction...but, as always, the Decepticons went back on their word. The Doctor was there, and he made the decision to send the Underbase into space, and destroy it." Optimus answered.

"Sounds like the choice you and Celestia would make..." Shining muttered.

"But the choice was not _his_ to make, and _that_ is his crime. If the Doctor should return to Equestria, I would like him turned over to the Cybertronian court to be given a trial proper."

Optimus turned to Celestia, and it was clear he himself was not happy about what he was going to say. "And should he return, I will have no choice to charge the Equestrian Government with aiding a war criminal."

Celestia nodded somberly and saluted. "Understood, Your Primeship."

* * *

"You've really got to see this." Cadence assured Twilight, helping the Terrorpony up the naturally formed ice sculpture. "It's beautiful."

"I don't see how a sword could be beautiful." Twilight responded.

"Oh, trust me, Twilight." Cadence answered. "You will when you see it. I don't even think Optimus could lift it. It's nearly as big as him!"

"I don't know...Optimus is pretty strong." Twilight mumbled, looking around for the sword Cadence had been gushing about since they beat Thunderwing. "...Where is it?"

"Where's what?"

"Where's the sword?"

"It's right-...here!" Cadence looked up and her jaw dropped.

Inside the glacier, there was nothing. Unless the huge gash in the ice where the sword used to be counted.

"It- it was right here!" Cadence exclaimed.

"I believe you, Cadence, but whatever was here, it's gone now." Twilight said, turning and walking away. Cadence felt devastated. That sword was so pretty...Twilight and Shining should've gotten to see it.

Perhaps if she had looked up instead of drooping her head low as she walked away, she would've noticed the shadow atop the glacier, holding that very sword in its hands. The shadow turned and ran off, its footsteps echoing like a Cybertronian's, but Cadence still didn't notice anything.

* * *

Meanwhile, at the Autobot base, Trixie was on the phone, making a call on behalf of her new, unexpected friend.

"Yes, hello...my name is Trixie. Is this Sparkplug and Son Salvage? It is? Oh, good. Yes, yes, Trixie has a job for you."

Trixie sighed.

"Yes, Trixie has a penchant to refer to herself in the third person. Anyways..."

Trixie took another glance at Thunderwing's remains, dragged in through the Bridge with an invisibility spell cloaking it at first, before Trixie dispelled it.

"Trixie and her friend have a scrap job for you..."

* * *

**Author's Notes for "Dark Envoy"**

**Don't think you've seen the last of Thunderwing!**

**A Guest review asked for me to make the Doctor and Optimus meet like old friends. I had already thought of the Doctor avoiding Optimus because of The Doctor doing what he done did on Cybertron before that reviewer asked for that.**

**Also, some things for "Infiltration" (which has since been published) are here in this chapter; The Doctor, the Star Saber, and the referring to Optimus as "Your Primeship.", Also Optimus telling Celestia he'll have to press charges if they don't report the Doctor next time?**

**_Politics_. Politics will be in Infiltration.  
**


End file.
